[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"        "-oTCOAD-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/COAD-TP/11541421/COAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COAD-TP/11548514/transformed.cor.cli.txt"

nPatients in clinical file=449, in cluster file=450, common to both=439
[1]  68 439
[1] "AMP PEAK  1(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           88                           351 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           88                           351 
[1] "AMP PEAK  2(5P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           86                           353 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           86                           353 
[1] "AMP PEAK  3(5Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           43                           396 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           43                           396 
[1] "AMP PEAK  4(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           94                           345 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           94                           345 
[1] "AMP PEAK  5(7P21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                          249                           190 
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                          249                           190 
[1] "AMP PEAK  6(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           155                            284 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           155                            284 
[1] "AMP PEAK  7(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           184                            255 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           184                            255 
[1] "AMP PEAK  8(8Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                          230                           209 
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                          230                           209 
[1] "AMP PEAK  9(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           254                            185 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           254                            185 
[1] "AMP PEAK 10(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                            90                            349 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                            90                            349 
[1] "AMP PEAK 11(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                            110                             329 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                            110                             329 
[1] "AMP PEAK 12(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            267                             172 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            267                             172 
[1] "AMP PEAK 13(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                           271                            168 
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                           271                            168 
[1] "AMP PEAK 14(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                           122                            317 
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                           122                            317 
[1] "AMP PEAK 15(16Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                           108                            331 
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                           108                            331 
[1] "AMP PEAK 16(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                            43                            396 
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                            43                            396 
[1] "AMP PEAK 17(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                         111                          328 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                         111                          328 
[1] "AMP PEAK 18(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                           102                            337 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                           102                            337 
[1] "AMP PEAK 19(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            73                            366 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            73                            366 
[1] "AMP PEAK 20(19Q13.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                             92                             347 
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                             92                             347 
[1] "AMP PEAK 21(20P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                           203                            236 
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                           203                            236 
[1] "AMP PEAK 22(20P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                            244                             195 
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                            244                             195 
[1] "AMP PEAK 23(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                            313                             126 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                            313                             126 
[1] "AMP PEAK 24(20Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                         314                          125 
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                         314                          125 
[1] "AMP PEAK 25(20Q13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                            317                             122 
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                            317                             122 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           163                            276 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           163                            276 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        119                         320 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        119                         320 
[1] "DEL PEAK  3(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          114                           325 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          114                           325 
[1] "DEL PEAK  4(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                         52                         387 
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                         52                         387 
[1] "DEL PEAK  5(2P21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         16                         423 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         16                         423 
[1] "DEL PEAK  6(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           24                           415 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           24                           415 
[1] "DEL PEAK  7(3P26.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                           69                           370 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                           69                           370 
[1] "DEL PEAK  8(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           85                           354 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           85                           354 
[1] "DEL PEAK  9(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            44                            395 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            44                            395 
[1] "DEL PEAK 10(4P16.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                          130                           309 
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                          130                           309 
[1] "DEL PEAK 11(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          142                           297 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          142                           297 
[1] "DEL PEAK 12(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          150                           289 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          150                           289 
[1] "DEL PEAK 13(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                          100                           339 
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                          100                           339 
[1] "DEL PEAK 14(5Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                          121                           318 
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                          121                           318 
[1] "DEL PEAK 15(5Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                          125                           314 
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                          125                           314 
[1] "DEL PEAK 16(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           54                           385 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           54                           385 
[1] "DEL PEAK 17(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         61                         378 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         61                         378 
[1] "DEL PEAK 18(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           12                           427 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           12                           427 
[1] "DEL PEAK 19(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                          183                           256 
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                          183                           256 
[1] "DEL PEAK 20(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        196                         243 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        196                         243 
[1] "DEL PEAK 21(8Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           30                           409 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           30                           409 
[1] "DEL PEAK 22(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           59                           380 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           59                           380 
[1] "DEL PEAK 23(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            77                            362 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            77                            362 
[1] "DEL PEAK 24(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            94                            345 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            94                            345 
[1] "DEL PEAK 25(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            105                             334 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            105                             334 
[1] "DEL PEAK 26(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           106                            333 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           106                            333 
[1] "DEL PEAK 27(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            57                            382 
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            57                            382 
[1] "DEL PEAK 28(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                           144                            295 
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                           144                            295 
[1] "DEL PEAK 29(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                           170                            269 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                           170                            269 
[1] "DEL PEAK 30(15Q15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                           164                            275 
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                           164                            275 
[1] "DEL PEAK 31(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                           162                            277 
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                           162                            277 
[1] "DEL PEAK 32(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                            154                             285 
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                            154                             285 
[1] "DEL PEAK 33(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                            54                            385 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                            54                            385 
[1] "DEL PEAK 34(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                            58                            381 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                            58                            381 
[1] "DEL PEAK 35(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                         245                          194 
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                         245                          194 
[1] "DEL PEAK 36(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                            68                            371 
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                            68                            371 
[1] "DEL PEAK 37(18P11.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                            239                             200 
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                            239                             200 
[1] "DEL PEAK 38(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                           266                            173 
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                           266                            173 
[1] "DEL PEAK 39(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                           280                            159 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                           280                            159 
[1] "DEL PEAK 40(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                            61                            378 
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                            61                            378 
[1] "DEL PEAK 41(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE 
                            83                            356 
  DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE 
                            83                            356 
[1] "DEL PEAK 42(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE 
                           136                            303 
  DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE 
                           136                            303 
[1] "DEL PEAK 43(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE 
                            153                             286 
  DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE 
                            153                             286 
[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] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 439 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
         154          160         1126         1419         1331         1321 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
         711          541         1286         1366         1068         1387 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
          NA          472         1127         1133          488         1054 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
        1111           NA          987         1001          962          926 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
         888         1020          718          672          671          995 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
         887          824          685          734          255          763 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
         766          735          627          662          751          742 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
         726          612          598          617           NA           NA 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
          NA         1595          293           NA           31           NA 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
          31         1127           31         1065         1765         1946 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
         212           31           NA         1186           31          276 
TCGA-AA-3520 TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
         731           NA         1127         1096          245          580 
TCGA-AA-3527 TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
          NA           NA          580         1035          882          882 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
         791          395           30          426         1034          639 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
          NA          730          546          911          700          638 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
         608          424          608         1856         2375          184 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
         212         1643           NA          426           28         1522 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3684 
        1431         1430          457           NA          182           NA 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3693 TCGA-AA-3695 TCGA-AA-3696 
        1127          578           NA           NA           NA           NA 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3712 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        2587          821           NA          579           30           30 
TCGA-AA-3812 TCGA-AA-3814 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        1066           NA           NA          761           31          547 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 
         485         1186         1124         1126          454           NA 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
         518           30           NA         1006           NA         1096 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
         975           30          945          945         1612          518 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 
         731           NA          912           NA          549          943 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
          NA          395          730         1004          791          730 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
          NA          638         1035           61          669          489 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
        1551          397         1036          791          761          730 
TCGA-AA-3982 TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
         822           NA          580           NA          822          424 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
        1157          578          913         1035          549          549 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
         518           NA          822         1278           30          518 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
         456          669         1064          457          457           30 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
         974          365          943          943           NA           31 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1065           31         1005         1065          791         1126 
TCGA-AA-A022 TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
          NA           NA         1581           NA         1216           NA 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
          NA           28           NA         1247         1216           NA 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
        1246            2          650          128         1720           24 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
          22           48           31            3           23            6 
TCGA-AD-A5EJ TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
          NA           13           14           28          441          824 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
          NA           NA          479            6          652          542 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
         158          168          209         2289         1532         1776 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
          NA           NA         1002           NA         2549           NA 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
        1977           NA         1868           NA           NA           NA 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
          NA           NA           NA           NA           NA           NA 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
          68           93           65           99          100            2 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
           8           10            3           41          534         3116 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
        1227         2134          475         1466         1561          669 
TCGA-CK-5915 TCGA-CK-5916 TCGA-CK-6746 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
          NA           NA           NA           89           61         3780 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
         701          609         1126          244          792          244 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
         822          396          884          670          699          915 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
         487          457           NA          457          457          518 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
         457          365          427          883          488          669 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
         456          395          396          457          427          335 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
         394          397          337          337          335          306 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
         366          456          373          596          411          350 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
         614          621          540          555           40          241 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
         460          543          137          521          380          491 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
         474          229          377          308          378          435 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
         275          287          354          408           46          365 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
         346          312         3641          743         1162         3974 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
        2821         1518          405          383         4270          228 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        1348         4000         4126          236         4233          186 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
         427          805         2475         3648         1094         1849 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
        3561         2988         2895           NA          407           NA 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
         415          409           NA         1091           47          496 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
         900          494         1024           39           16         1077 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
         591         3275           NA          254         2506           NA 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
        2268         1310         1882         1631         1359         1674 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
        1574         1372         1199         1093         1117         1095 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
         804          672          792          419         1089          796 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
        2792           NA         1434         1606          125           NA 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
         320           85          182          170           40          158 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
         167          821          526          202          449          921 
TCGA-WS-AB45 
        2038 
Variable 1:'AGE':	nDistinctValues=58,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=79,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=280,	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=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	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=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=22,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 439 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=58, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 11  76 300  51 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 11  76 300  51 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
 11  76 300  51 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 11  76 300  51 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
256 103  79 
[1] "table(vv)"
vv
 N0  N1  N2 
256 103  79 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2 
256 103  79 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
256 103  79 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=21, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(2Q33.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(2Q33.1) MUTATED    62  20
  AMP PEAK  1(2Q33.1) WILD-TYPE 273  67
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           82                           340 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                           20                            67 
$`AMP PEAK  1(2Q33.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
        5.06        37.02        34.65        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 
       30.44        32.71        29.16        24.16        24.69        23.87 
TCGA-A6-A566 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3562 
       24.92         1.02        34.03        29.00        29.00        19.99 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3812 
       50.04        15.02        37.05         5.03         0.99        35.05 
TCGA-AA-3851 TCGA-AA-3867 TCGA-AA-3971 TCGA-AA-3979 TCGA-AA-A00W TCGA-AA-A01I 
       33.07        24.03        16.08        24.00        14.99        31.00 
TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02E TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 
        1.02        26.01         2.96        21.37         4.21         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-6196 
        1.02         0.10         0.20         0.43        16.31         0.20 
TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4950 
        6.87         5.13         3.19         0.07         0.26        40.34 
TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       21.99         8.02        29.06         5.03        17.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5541 
       14.04        29.03        21.99        14.99        14.99        11.51 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6898 TCGA-DM-A0XD TCGA-DM-A1DA TCGA-DM-A280 
        4.50        17.13         7.53        24.43         7.50         7.76 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6295 
       14.04        26.47        35.97         8.61         1.55         8.35 
TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       74.56        45.11        39.42        47.15        52.80         4.11 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-RU-A8FL 
        1.32         5.19        17.29        30.28 

$`AMP PEAK  1(2Q33.1) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.26        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5660 
       37.05        37.25        16.04        32.45        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 
       24.39        20.12        19.66        20.28        16.24        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       37.05        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 
       36.03         8.05        19.07        19.07        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.05        47.01        11.01         5.98 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00        85.05        26.99        19.04         0.99 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       36.95        37.02        14.93        17.03         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        25.02        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       33.04        35.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05        40.96         0.07        56.55         0.79         0.72 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.76         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
       15.75        21.44        17.82         5.19         5.52        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 
       50.37        58.39         1.41         5.65        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       12.10       100.01        29.56         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 
        2.24         3.06         2.14         3.25         3.29         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
        0.10         1.35        17.56       102.44        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       48.20        51.32        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02         8.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       15.02        15.02        12.00        16.04        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       13.51        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
        7.92        15.12        17.85        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       12.59       140.38        44.32       131.51       135.65       139.17 
TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        6.12        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
        0.53        35.41        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       23.51        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       51.75        35.93        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       10.98        10.52         2.79         5.98         5.59         5.49 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
       26.99         6.64        14.76        67.00 

  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                        74.56                        140.38 
  AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE 
                        16.67                         20.07 
[1] "0.1 - 74.6 (16.7)"  "0.1 - 140.4 (20.1)"
[1] "hr=" "1.7"
D1V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  1(2Q33.1) MUTATED        13        0        5        19         0
  AMP PEAK  1(2Q33.1) WILD-TYPE      59        1       23       112         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(2Q33.1) MUTATED           1         5          3         14
  AMP PEAK  1(2Q33.1) WILD-TYPE         0        16          9         41
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  1(2Q33.1) MUTATED           11        9         4         1
  AMP PEAK  1(2Q33.1) WILD-TYPE         27       34        14         1
D1V3, multiclass
            clus
vv           AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  STAGE I                             13                            59
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           19                           112
  STAGE IIB                            0                             8
  STAGE IIC                            1                             0
  STAGE III                            5                            16
  STAGE IIIA                           3                             9
  STAGE IIIB                          14                            41
  STAGE IIIC                          11                            27
  STAGE IV                             9                            34
  STAGE IVA                            4                            14
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  1(2Q33.1) MUTATED     3  14  62   9
  AMP PEAK  1(2Q33.1) WILD-TYPE   8  62 238  42
D1V4, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  T1                           3                             8
  T2                          14                            62
  T3                          62                           238
  T4                           9                            42
[1] 4 2
[1] 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
  AMP PEAK  1(2Q33.1) MUTATED    41  22  24
  AMP PEAK  1(2Q33.1) WILD-TYPE 215  81  55
D1V5, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  N0                          41                           215
  N1                          22                            81
  N2                          24                            55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  1(2Q33.1) MUTATED    57  11   2   1  16
  AMP PEAK  1(2Q33.1) WILD-TYPE 263  41   6   1  34
D1V6, multiclass
     clus
vv    AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  M0                           57                           263
  M1                           11                            41
  M1A                           2                             6
  M1B                           1                             1
  MX                           16                            34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    38  50
  AMP PEAK  1(2Q33.1) WILD-TYPE 169 182
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     38   50
  AMP PEAK  1(2Q33.1) WILD-TYPE  169  182
        clus
vv       AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  FEMALE                          38                           169
  MALE                            50                           182
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED    79   9
  AMP PEAK  1(2Q33.1) WILD-TYPE 299  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED     79    9
  AMP PEAK  1(2Q33.1) WILD-TYPE  299   50
                               clus
vv                              AMP PEAK  1(2Q33.1) MUTATED
  COLON ADENOCARCINOMA                                   79
  COLON MUCINOUS ADENOCARCINOMA                           9
                               clus
vv                              AMP PEAK  1(2Q33.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    299
  COLON MUCINOUS ADENOCARCINOMA                            50
[1] 2 2
[1] FALSE
D1V9, binary
                               cls
clus                              0   1
  AMP PEAK  1(2Q33.1) MUTATED     1  87
  AMP PEAK  1(2Q33.1) WILD-TYPE   2 349
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(2Q33.1) MUTATED      1   87
  AMP PEAK  1(2Q33.1) WILD-TYPE    2  349
     clus
vv    AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  NO                            1                             2
  YES                          87                           349
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(2Q33.1) MUTATED    55   2   6   6
  AMP PEAK  1(2Q33.1) WILD-TYPE 258   1  18  19
D1V10, multiclass
    clus
vv   AMP PEAK  1(2Q33.1) MUTATED AMP PEAK  1(2Q33.1) WILD-TYPE
  R0                          55                           258
  R1                           2                             1
  R2                           6                            18
  RX                           6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(2Q33.1) MUTATED                                  1     2
  AMP PEAK  1(2Q33.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(2Q33.1) MUTATED                          13    47
  AMP PEAK  1(2Q33.1) WILD-TYPE                        37   164
D1V12, multiclass
                                  clus
vv                                 AMP PEAK  1(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                     47
                                  clus
vv                                 AMP PEAK  1(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   37
  WHITE                                                      164
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(5P13.2) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(5P13.2) MUTATED    66  18
  AMP PEAK  2(5P13.2) WILD-TYPE 269  69
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           84                           338 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                           18                            69 
$`AMP PEAK  2(5P13.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 
        5.06        43.76        43.43        44.91        45.60        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6650 TCGA-A6-6651 TCGA-AA-3488 
       34.65        32.45        30.44        20.61        21.76         5.03 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3666 
       26.01        12.99        13.02        24.00        19.99         2.01 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3842 
       47.01         5.98        37.05        19.00         0.99        37.02 
TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3966 
       14.93        36.03         0.99        17.03        24.03         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00Z TCGA-AA-A01D 
       21.99        50.99        26.01        34.03        21.99         0.99 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 
       51.98         2.96         2.01        41.00        40.96         1.58 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-5403 TCGA-AZ-6598 
        0.43         0.92         0.20         6.87        62.79        49.41 
TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-4752 
       29.56         1.94         2.24        48.20         8.02        13.02 
TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6169 
       16.01        15.02        14.04        29.03        14.99        13.02 
TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6538 TCGA-D5-6898 TCGA-D5-6924 
       11.01        19.59        17.75        17.13         7.53        14.30 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 
       13.41        12.00        11.38        12.59         7.50         6.12 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6297 
       98.24        95.18        13.38         1.55        35.41        82.39 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-RU-A8FL 
       91.79        46.75        47.15         1.32         6.64        30.28 

$`AMP PEAK  2(5P13.2) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.26        37.02        46.65        23.38        17.79        42.28 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3810 
       35.11        13.94        15.52        37.05        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       14.53        32.91        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84        52.44         9.63         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        29.00         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 
       21.01        17.95        29.95        23.01        20.98        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        50.04        47.05        15.02        11.01 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
       36.00         5.03        85.05        26.99        19.04         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       38.99        36.95        17.03         0.99        33.07        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        31.07        53.00        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       24.00         2.01        20.98        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         5.03         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 
        1.02         0.10         0.76         0.20         0.46        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13        83.80        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         3.06         2.14         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04         8.02        27.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       12.00        16.04        21.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       11.01        12.95        13.05        11.08        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        14.99        12.26        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25         1.32         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
        4.50        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 
       12.43         9.04         9.44        11.64         1.51        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       13.32       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       60.79       117.07         8.61        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        1.28         0.53        19.43       107.67        28.21         8.35 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        51.75        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       26.17        52.80         4.11        10.98        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.98         5.59         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       14.76        67.00 

  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                         0.20                          0.07 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                        98.24                        140.38 
  AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE 
                        17.44                         20.07 
[1] "0.2 - 98.2 (17.4)"  "0.1 - 140.4 (20.1)"
[1] "hr=" "1.1"
D2V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  2(5P13.2) MUTATED        14        0        5        22         1
  AMP PEAK  2(5P13.2) WILD-TYPE      58        1       23       109         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(5P13.2) MUTATED           0         3          4          6
  AMP PEAK  2(5P13.2) WILD-TYPE         1        18          8         49
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(5P13.2) MUTATED           13       12         3         1
  AMP PEAK  2(5P13.2) WILD-TYPE         25       31        15         1
D2V3, multiclass
            clus
vv           AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  STAGE I                             14                            58
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           22                           109
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           4                             8
  STAGE IIIB                           6                            49
  STAGE IIIC                          13                            25
  STAGE IV                            12                            31
  STAGE IVA                            3                            15
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  2(5P13.2) MUTATED     1  18  60   7
  AMP PEAK  2(5P13.2) WILD-TYPE  10  58 240  44
D2V4, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  T1                           1                            10
  T2                          18                            58
  T3                          60                           240
  T4                           7                            44
[1] 4 2
[1] 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
  AMP PEAK  2(5P13.2) MUTATED    42  20  24
  AMP PEAK  2(5P13.2) WILD-TYPE 214  83  55
D2V5, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  N0                          42                           214
  N1                          20                            83
  N2                          24                            55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  2(5P13.2) MUTATED    56  13   2   1  11
  AMP PEAK  2(5P13.2) WILD-TYPE 264  39   6   1  39
D2V6, multiclass
     clus
vv    AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  M0                           56                           264
  M1                           13                            39
  M1A                           2                             6
  M1B                           1                             1
  MX                           11                            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"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    44  42
  AMP PEAK  2(5P13.2) WILD-TYPE 163 190
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     44   42
  AMP PEAK  2(5P13.2) WILD-TYPE  163  190
        clus
vv       AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  FEMALE                          44                           163
  MALE                            42                           190
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED    74  12
  AMP PEAK  2(5P13.2) WILD-TYPE 304  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED     74   12
  AMP PEAK  2(5P13.2) WILD-TYPE  304   47
                               clus
vv                              AMP PEAK  2(5P13.2) MUTATED
  COLON ADENOCARCINOMA                                   74
  COLON MUCINOUS ADENOCARCINOMA                          12
                               clus
vv                              AMP PEAK  2(5P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    304
  COLON MUCINOUS ADENOCARCINOMA                            47
[1] 2 2
[1] FALSE
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(5P13.2) MUTATED     0  86
  AMP PEAK  2(5P13.2) WILD-TYPE   3 350
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(5P13.2) MUTATED      0   86
  AMP PEAK  2(5P13.2) WILD-TYPE    3  350
     clus
vv    AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  NO                            0                             3
  YES                          86                           350
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(5P13.2) MUTATED    63   0   8   2
  AMP PEAK  2(5P13.2) WILD-TYPE 250   3  16  23
D2V10, multiclass
    clus
vv   AMP PEAK  2(5P13.2) MUTATED AMP PEAK  2(5P13.2) WILD-TYPE
  R0                          63                           250
  R1                           0                             3
  R2                           8                            16
  RX                           2                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(5P13.2) MUTATED                                  1     1
  AMP PEAK  2(5P13.2) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(5P13.2) MUTATED                          11    41
  AMP PEAK  2(5P13.2) WILD-TYPE                        39   170
D2V12, multiclass
                                  clus
vv                                 AMP PEAK  2(5P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     41
                                  clus
vv                                 AMP PEAK  2(5P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   39
  WHITE                                                      170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(5Q22.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(5Q22.3) MUTATED    35   7
  AMP PEAK  3(5Q22.3) WILD-TYPE 300  80
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           42                           380 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                            7                            80 
$`AMP PEAK  3(5Q22.3) MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 
        5.06        44.91        45.60        37.25        34.65        32.45 
TCGA-A6-6142 TCGA-A6-6650 TCGA-AA-3488 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3715 
       25.08        20.61         5.03        15.02         5.98         0.99 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       14.93        24.03        12.99        13.05        34.06        26.01 
TCGA-AA-3994 TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-4684 
       27.02        40.96         1.58         0.43        15.75        65.00 
TCGA-AZ-6598 TCGA-AZ-6606 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-6161 TCGA-CM-6163 
       49.41        11.74        16.01         5.03        15.02        14.04 
TCGA-CM-6167 TCGA-CM-6678 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6932 TCGA-DM-A1D0 
       14.99        11.01        17.75         1.32        11.38       130.65 
TCGA-DM-A1D8 TCGA-DM-A28M TCGA-F4-6460 TCGA-G4-6306 TCGA-G4-6627 TCGA-NH-A6GB 
       12.59        95.18        13.38        44.68        47.15         5.59 

$`AMP PEAK  3(5Q22.3) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.26        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       17.79        42.28        35.11        13.94        15.52        37.05 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.04        36.53        14.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       29.16        27.09        22.52        24.13         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.05        47.01        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
        5.03        85.05        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       36.95        37.02        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       27.02        29.98        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3977 TCGA-AA-3979 
        2.01        21.99        16.08        50.99        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        2.96        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95         0.20        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        83.80        22.36        62.79        61.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        6.77        12.10       100.01        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        1.94         2.24         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02         8.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        17.03        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       14.99        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.42        18.25         7.92        15.12        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.41         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20        92.75        49.91        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24         8.61        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       61.87        53.62        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        46.75        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
        4.11        10.98        10.52         2.79         5.98         1.32 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19         5.49        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 
       30.28        67.00 

  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                         0.43                          0.07 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                       130.65                        140.38 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                       15.385                        20.005 
[1] "0.4 - 130.7 (15.4)" "0.1 - 140.4 (20.0)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  3(5Q22.3) MUTATED         6        0        2        11         1
  AMP PEAK  3(5Q22.3) WILD-TYPE      66        1       26       120         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(5Q22.3) MUTATED           0         1          1          4
  AMP PEAK  3(5Q22.3) WILD-TYPE         1        20         11         51
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  3(5Q22.3) MUTATED            5        6         5         0
  AMP PEAK  3(5Q22.3) WILD-TYPE         33       37        13         2
D3V3, multiclass
            clus
vv           AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  STAGE I                              6                            66
  STAGE IA                             0                             1
  STAGE II                             2                            26
  STAGE IIA                           11                           120
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            1                            20
  STAGE IIIA                           1                            11
  STAGE IIIB                           4                            51
  STAGE IIIC                           5                            33
  STAGE IV                             6                            37
  STAGE IVA                            5                            13
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  3(5Q22.3) MUTATED     1   7  29   6
  AMP PEAK  3(5Q22.3) WILD-TYPE  10  69 271  45
D3V4, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  T1                           1                            10
  T2                           7                            69
  T3                          29                           271
  T4                           6                            45
[1] 4 2
[1] 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
  AMP PEAK  3(5Q22.3) MUTATED    21  11  11
  AMP PEAK  3(5Q22.3) WILD-TYPE 235  92  68
D3V5, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  N0                          21                           235
  N1                          11                            92
  N2                          11                            68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  3(5Q22.3) MUTATED    26   8   3   0   4
  AMP PEAK  3(5Q22.3) WILD-TYPE 294  44   5   2  46
D3V6, multiclass
     clus
vv    AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  M0                           26                           294
  M1                            8                            44
  M1A                           3                             5
  M1B                           0                             2
  MX                            4                            46
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED    22  21
  AMP PEAK  3(5Q22.3) WILD-TYPE 185 211
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     22   21
  AMP PEAK  3(5Q22.3) WILD-TYPE  185  211
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  FEMALE                          22                           185
  MALE                            21                           211
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED    40   3
  AMP PEAK  3(5Q22.3) WILD-TYPE 338  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     40    3
  AMP PEAK  3(5Q22.3) WILD-TYPE  338   56
                               clus
vv                              AMP PEAK  3(5Q22.3) MUTATED
  COLON ADENOCARCINOMA                                   40
  COLON MUCINOUS ADENOCARCINOMA                           3
                               clus
vv                              AMP PEAK  3(5Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    338
  COLON MUCINOUS ADENOCARCINOMA                            56
[1] 2 2
[1] FALSE
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED     1  42
  AMP PEAK  3(5Q22.3) WILD-TYPE   2 394
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED      1   42
  AMP PEAK  3(5Q22.3) WILD-TYPE    2  394
     clus
vv    AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  NO                            1                             2
  YES                          42                           394
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(5Q22.3) MUTATED    29   0   5   0
  AMP PEAK  3(5Q22.3) WILD-TYPE 284   3  19  25
D3V10, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  R0                          29                           284
  R1                           0                             3
  R2                           5                            19
  RX                           0                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(5Q22.3) MUTATED                                  0     0
  AMP PEAK  3(5Q22.3) WILD-TYPE                                1    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(5Q22.3) MUTATED                           7    23
  AMP PEAK  3(5Q22.3) WILD-TYPE                        43   188
D3V12, multiclass
                                  clus
vv                                 AMP PEAK  3(5Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     23
                                  clus
vv                                 AMP PEAK  3(5Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   43
  WHITE                                                      188
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(6P21.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(6P21.1) MUTATED    72  18
  AMP PEAK  4(6P21.1) WILD-TYPE 263  69
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           90                           332 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           18                            69 
$`AMP PEAK  4(6P21.1) MUTATED`
TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       43.43        44.91        36.53        32.45        30.44        29.19 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A56B 
       22.52        25.08        25.18        20.61        23.87        52.44 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3561 
       29.00        29.00        12.99        13.02        24.00        13.94 
TCGA-AA-3562 TCGA-AA-3679 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3846 
       19.99        15.02        85.05         0.99        35.05        17.03 
TCGA-AA-3848 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3968 
        0.99        24.03        27.02         2.01        20.98        21.99 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A01I 
       27.02         7.96        13.94        34.03        27.02        31.00 
TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 
        2.96        40.96         1.02         0.20        14.50         0.95 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CA-6719 TCGA-CK-4952 
        0.20         5.19        22.36        65.00         1.35        15.62 
TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
       21.99         8.02        13.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-5539 
       16.01         5.03        15.02        13.02        15.02        19.59 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       11.51         1.32        15.12        17.13        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1DA 
       10.13         9.04        13.41        11.38        13.32         7.50 
TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       14.04       117.07        98.24        95.18         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6310 
       13.45         1.55         0.53        28.21        82.39        45.11 
TCGA-G4-6311 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-RU-A8FL 
       39.42        91.79        46.75        10.98         1.32        30.28 

$`AMP PEAK  4(6P21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.76        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       17.79        42.28        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 
       37.05        37.25        16.04        34.65        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 
       29.16        27.09        24.13         8.38        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.69        24.39        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       24.92        61.84         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
        6.97         1.02        13.02        38.99         1.02         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       34.03        26.01         0.99        14.01        33.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 
       17.95        29.95        23.01        20.98        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        0.92        50.04        47.05        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3854 
       38.99        36.95        37.02        14.93        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 
       26.01        24.00         2.01        34.03         2.01        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       19.07        27.02        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05        17.03         4.01        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         1.58         0.10         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 
        0.43         0.46         0.92        27.09        16.31        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82         5.52         6.87        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13        83.80 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        40.34        70.16 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       48.20        51.32        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02         8.02        26.04        27.02 
TCGA-CM-5344 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       22.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        14.99        12.26        13.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       20.19        20.42        17.75        18.25         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
        4.50        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
        6.12        26.47        81.37       119.93        35.97        60.79 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       11.11        13.64         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24        33.67         1.28        35.41        19.43       107.67 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        51.75        35.93        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       47.15        52.80         4.11        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       14.76        67.00 

  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                         0.20                          0.07 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                       117.07                        140.38 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                       17.080                        20.005 
[1] "0.2 - 117.1 (17.1)" "0.1 - 140.4 (20.0)"
[1] "hr=" "1"  
D4V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  4(6P21.1) MUTATED        12        0        1        24         1
  AMP PEAK  4(6P21.1) WILD-TYPE      60        1       27       107         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(6P21.1) MUTATED           0         4          6         15
  AMP PEAK  4(6P21.1) WILD-TYPE         1        17          6         40
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  4(6P21.1) MUTATED           12       10         6         1
  AMP PEAK  4(6P21.1) WILD-TYPE         26       33        12         1
D4V3, multiclass
            clus
vv           AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  STAGE I                             12                            60
  STAGE IA                             0                             1
  STAGE II                             1                            27
  STAGE IIA                           24                           107
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           6                             6
  STAGE IIIB                          15                            40
  STAGE IIIC                          12                            26
  STAGE IV                            10                            33
  STAGE IVA                            6                            12
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(6P21.1) MUTATED     2  13  70   9
  AMP PEAK  4(6P21.1) WILD-TYPE   9  63 230  42
D4V4, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  T1                           2                             9
  T2                          13                            63
  T3                          70                           230
  T4                           9                            42
[1] 4 2
[1] 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
  AMP PEAK  4(6P21.1) MUTATED    45  22  27
  AMP PEAK  4(6P21.1) WILD-TYPE 211  81  52
D4V5, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  N0                          45                           211
  N1                          22                            81
  N2                          27                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  4(6P21.1) MUTATED    66  12   4   1   8
  AMP PEAK  4(6P21.1) WILD-TYPE 254  40   4   1  42
D4V6, multiclass
     clus
vv    AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  M0                           66                           254
  M1                           12                            40
  M1A                           4                             4
  M1B                           1                             1
  MX                            8                            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"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED    39  55
  AMP PEAK  4(6P21.1) WILD-TYPE 168 177
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     39   55
  AMP PEAK  4(6P21.1) WILD-TYPE  168  177
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  FEMALE                          39                           168
  MALE                            55                           177
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED    85   8
  AMP PEAK  4(6P21.1) WILD-TYPE 293  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     85    8
  AMP PEAK  4(6P21.1) WILD-TYPE  293   51
                               clus
vv                              AMP PEAK  4(6P21.1) MUTATED
  COLON ADENOCARCINOMA                                   85
  COLON MUCINOUS ADENOCARCINOMA                           8
                               clus
vv                              AMP PEAK  4(6P21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    293
  COLON MUCINOUS ADENOCARCINOMA                            51
[1] 2 2
[1] FALSE
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED     3  91
  AMP PEAK  4(6P21.1) WILD-TYPE   0 345
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED      3   91
  AMP PEAK  4(6P21.1) WILD-TYPE    0  345
     clus
vv    AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  NO                            3                             0
  YES                          91                           345
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(6P21.1) MUTATED    67   0   7   4
  AMP PEAK  4(6P21.1) WILD-TYPE 246   3  17  21
D4V10, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  R0                          67                           246
  R1                           0                             3
  R2                           7                            17
  RX                           4                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(6P21.1) MUTATED                                  1     1
  AMP PEAK  4(6P21.1) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(6P21.1) MUTATED                           9    53
  AMP PEAK  4(6P21.1) WILD-TYPE                        41   158
D4V12, multiclass
                                  clus
vv                                 AMP PEAK  4(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     53
                                  clus
vv                                 AMP PEAK  4(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   41
  WHITE                                                      158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(7P21.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(7P21.2) MUTATED   189  50
  AMP PEAK  5(7P21.2) WILD-TYPE 146  37
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                          239                           183 
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                           50                            37 
$`AMP PEAK  5(7P21.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 
        5.06         5.26        37.02        43.76        43.43        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        45.60        13.94        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       29.16        22.52        24.13        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       20.61        24.69        23.87        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 
       52.44         9.63         5.03         1.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        35.01        58.03         6.97        38.99         9.07 
TCGA-AA-3524 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       36.03        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       13.02        24.00        19.99        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3679 TCGA-AA-3680 
        6.05        54.02         2.01        14.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
        0.99        35.05         0.99        36.95        37.02        14.93 
TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
        0.99        32.05         0.99        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3950 
       27.02        29.98        18.05        31.00        24.00        24.00 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3982 
       20.98        21.99        16.08        34.06        26.01        27.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q 
       27.02        13.94        19.00        34.03        17.03        42.02 
TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01X 
       17.03        15.02        32.02        35.01        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y 
       37.02        51.98         2.01         5.03         0.92        39.98 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37         4.21         0.79         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        0.10         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
        0.95        15.75         0.20        17.82         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       75.25        50.37        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19         1.94         3.06         2.14         3.25         3.29 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 
        1.35        17.56       102.44        40.34        21.99        20.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        8.02         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        16.01         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        11.01        11.08        11.08        11.01        10.06 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        11.51        17.75         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.50        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XD 
       12.43        14.30         9.04        13.41        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F 
       44.32       131.51         7.76         6.12        14.04        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 
      117.07        95.18         8.61        13.38        13.45         1.55 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
       33.67         0.53        35.41       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       23.51        74.56        61.87        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6323 
       39.42        35.93        36.72        36.00        26.43        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB 
       91.79        46.75        47.15         4.11         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 
        1.32         5.19         6.64        30.28        67.00 

$`AMP PEAK  5(7P21.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-2684 
       46.65        23.38        17.79        42.28        15.52        37.05 
TCGA-A6-4105 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       14.53        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       27.09         8.38        21.76        24.39        20.12        19.66 
TCGA-A6-A567 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       61.84         3.02        63.98         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       29.00         0.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       20.98        13.94         6.97         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 TCGA-AA-3821 
       47.01        26.99        19.04         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 
       17.98        15.95        38.99        17.03        33.07        36.03 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       31.07        53.00         2.01        12.99        33.01        26.01 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 
        2.01        34.03         2.01        50.99        13.05        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       24.00        19.07         7.96        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
       18.05         4.01        27.02         0.99        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02         0.99        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02E 
       38.07         1.02         1.02        35.01        39.06         2.96 
TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
       39.98        22.03        41.00        18.05         0.07        56.55 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A69D 
        0.72         0.76         0.92        27.09        21.44         5.52 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-6599 
       58.39         1.41         5.65        32.94         5.13         6.77 
TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
      100.01         2.24         0.07         0.26         0.33         0.10 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        48.20        51.32        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5349 
        2.01       124.27        23.05        37.02        26.04        30.08 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        21.99        13.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 
       13.05        12.03        14.99        12.26        13.51        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       20.42        18.25        16.14        15.58        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D0 
       11.64         1.51        12.00        11.38       119.70       130.65 
TCGA-DM-A1D7 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
       13.32       135.65       139.17        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       60.79        98.24        11.11        13.64         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 
       16.31        29.59        16.24         1.28        19.43         8.35 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 
       43.07        53.62        51.75        22.09        26.04        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A8F8 
       26.17        52.80        10.98        10.52         2.79         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
       26.99        17.29        14.76 

  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                       140.38                        139.17 
  AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE 
                        19.99                         19.43 
[1] "0.1 - 140.4 (20.0)" "0.1 - 139.2 (19.4)"
[1] "hr=" "1"  
D5V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  5(7P21.2) MUTATED        39        1       15        54         2
  AMP PEAK  5(7P21.2) WILD-TYPE      33        0       13        77         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(7P21.2) MUTATED           0        13         11         37
  AMP PEAK  5(7P21.2) WILD-TYPE         1         8          1         18
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  5(7P21.2) MUTATED           26       30        14         1
  AMP PEAK  5(7P21.2) WILD-TYPE         12       13         4         1
D5V3, multiclass
            clus
vv           AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  STAGE I                             39                            33
  STAGE IA                             1                             0
  STAGE II                            15                            13
  STAGE IIA                           54                            77
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                           13                             8
  STAGE IIIA                          11                             1
  STAGE IIIB                          37                            18
  STAGE IIIC                          26                            12
  STAGE IV                            30                            13
  STAGE IVA                           14                             4
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  5(7P21.2) MUTATED     9  41 170  28
  AMP PEAK  5(7P21.2) WILD-TYPE   2  35 130  23
D5V4, multiclass
    clus
vv   AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  T1                           9                             2
  T2                          41                            35
  T3                         170                           130
  T4                          28                            23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  5(7P21.2) MUTATED   122  70  56
  AMP PEAK  5(7P21.2) WILD-TYPE 134  33  23
D5V5, multiclass
    clus
vv   AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  N0                         122                           134
  N1                          70                            33
  N2                          56                            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                             M0  M1 M1A M1B  MX
  AMP PEAK  5(7P21.2) MUTATED   170  36   7   1  31
  AMP PEAK  5(7P21.2) WILD-TYPE 150  16   1   1  19
D5V6, multiclass
     clus
vv    AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  M0                          170                           150
  M1                           36                            16
  M1A                           7                             1
  M1B                           1                             1
  MX                           31                            19
[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"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.2) MUTATED   117 132
  AMP PEAK  5(7P21.2) WILD-TYPE  90 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.2) MUTATED    117  132
  AMP PEAK  5(7P21.2) WILD-TYPE   90  100
        clus
vv       AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  FEMALE                         117                            90
  MALE                           132                           100
[1] 2 2
[1] FALSE
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.2) MUTATED   222  26
  AMP PEAK  5(7P21.2) WILD-TYPE 156  33
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.2) MUTATED    222   26
  AMP PEAK  5(7P21.2) WILD-TYPE  156   33
                               clus
vv                              AMP PEAK  5(7P21.2) MUTATED
  COLON ADENOCARCINOMA                                  222
  COLON MUCINOUS ADENOCARCINOMA                          26
                               clus
vv                              AMP PEAK  5(7P21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    156
  COLON MUCINOUS ADENOCARCINOMA                            33
[1] 2 2
[1] FALSE
D5V9, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.2) MUTATED     3 246
  AMP PEAK  5(7P21.2) WILD-TYPE   0 190
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.2) MUTATED      3  246
  AMP PEAK  5(7P21.2) WILD-TYPE    0  190
     clus
vv    AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  NO                            3                             0
  YES                         246                           190
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(7P21.2) MUTATED   178   2  16  10
  AMP PEAK  5(7P21.2) WILD-TYPE 135   1   8  15
D5V10, multiclass
    clus
vv   AMP PEAK  5(7P21.2) MUTATED AMP PEAK  5(7P21.2) WILD-TYPE
  R0                         178                           135
  R1                           2                             1
  R2                          16                             8
  RX                          10                            15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(7P21.2) MUTATED                                  1     5
  AMP PEAK  5(7P21.2) WILD-TYPE                                0     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(7P21.2) MUTATED                          33   124
  AMP PEAK  5(7P21.2) WILD-TYPE                        17    87
D5V12, multiclass
                                  clus
vv                                 AMP PEAK  5(7P21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 33
  WHITE                                                    124
                                  clus
vv                                 AMP PEAK  5(7P21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                       87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(8P11.23) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(8P11.23) MUTATED   118  27
  AMP PEAK  6(8P11.23) WILD-TYPE 217  60
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           145                            277 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                            27                             60 
$`AMP PEAK  6(8P11.23) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 
        5.06         5.26        43.43        17.79        45.60        13.94 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       34.65        32.45        32.91        32.71        29.16        27.09 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6782 TCGA-A6-A5ZU TCGA-AA-3495 TCGA-AA-3496 
       25.18        24.16        20.28         9.63        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3534 
       35.01         6.97         1.02        36.03        19.07        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 
       26.01        12.99        33.99        20.98        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 
        5.98        37.05        19.00         5.03        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 
        0.99        36.95        17.03        31.07        31.07        24.03 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-A00K 
       18.05        12.99        24.00        34.06        24.00        18.05 
TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 
        0.99        21.99         0.99         1.02        37.02        51.98 
TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-6004 
        0.92         0.07         1.58         0.10         0.43        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       16.31        21.44         5.19         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6607 
       83.80        22.36        62.79        61.41        49.41         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         2.14         3.29         0.07 
TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 
      102.44        15.62        48.20        51.32         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       37.02         8.02         8.02        22.98        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 
        5.03        15.02        15.02        15.02        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 
       14.99        12.99        13.02        11.01        11.08        11.08 
TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 
       10.06        11.51        20.19         1.32         4.50        17.13 
TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 
       16.14         7.53        12.43        14.30         9.04        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 
       10.26       119.70        38.20         7.50        44.32         6.12 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6302 
      117.07        98.24        13.45         6.18        16.24        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 
       61.87        53.62        45.11        39.42        26.43        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       47.15         4.11         5.59        17.29         6.64        30.28 
TCGA-WS-AB45 
       67.00 

$`AMP PEAK  6(8P11.23) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       37.02        46.65        43.76        23.38        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       35.11        15.52        37.05        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       14.53        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        22.52        24.13         8.38        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 
       19.66        16.24        24.92        61.84        52.44         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
        1.02         3.02         1.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       19.07        34.03        29.00         0.99        14.01        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 
       13.02        24.00        17.95        29.95        23.01        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
       13.94        61.02         2.01         0.92        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01        36.00        85.05        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       14.93         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 
        2.01        21.99        16.08        50.99        13.05        26.01 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       38.04        19.00        30.02        34.03        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        27.02        42.02        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R 
       39.06         2.96        39.98         2.01         5.03        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        18.05        40.96        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.79         0.72         1.02         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46         0.92        14.50         0.95        15.75         0.20 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.52         6.87        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
        1.41        65.00         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        5.23        11.74         3.25         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 
        1.35        17.56        40.34        70.16        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
        2.93       124.27        23.05        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 
       29.06        22.03        30.08        17.03        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 
       16.04        15.02        14.04        12.95        13.05        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 
       12.03        14.99        12.26        19.59        13.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       17.75        18.25         7.92        15.12        17.85        12.49 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       15.58        12.39        10.13         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
        1.51        12.00        24.43       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       13.32        12.59       140.38       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       60.79        95.18         8.61        13.38        11.11        13.64 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
       35.87         1.55        16.31        29.59        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       82.39        23.51        74.56        44.68        55.04        51.75 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        36.00        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V 
       35.80        26.17        91.79        52.80        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         1.32         5.19         5.49        26.99 
TCGA-QG-A5Z2 
       14.76 

  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                        119.70                         140.38 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                         17.29                          21.01 
[1] "0.1 - 119.7 (17.3)" "0.1 - 140.4 (21.0)"
[1] "hr=" "1.1"
D6V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  6(8P11.23) MUTATED        31        0       15        39         3
  AMP PEAK  6(8P11.23) WILD-TYPE      41        1       13        92         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(8P11.23) MUTATED           1         8          4         18
  AMP PEAK  6(8P11.23) WILD-TYPE         0        13          8         37
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  6(8P11.23) MUTATED           15       14         6         0
  AMP PEAK  6(8P11.23) WILD-TYPE         23       29        12         2
D6V3, multiclass
            clus
vv           AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  STAGE I                              31                             41
  STAGE IA                              0                              1
  STAGE II                             15                             13
  STAGE IIA                            39                             92
  STAGE IIB                             3                              5
  STAGE IIC                             1                              0
  STAGE III                             8                             13
  STAGE IIIA                            4                              8
  STAGE IIIB                           18                             37
  STAGE IIIC                           15                             23
  STAGE IV                             14                             29
  STAGE IVA                             6                             12
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  6(8P11.23) MUTATED     3  31 104  17
  AMP PEAK  6(8P11.23) WILD-TYPE   8  45 196  34
D6V4, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  T1                            3                              8
  T2                           31                             45
  T3                          104                            196
  T4                           17                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  6(8P11.23) MUTATED    94  33  28
  AMP PEAK  6(8P11.23) WILD-TYPE 162  70  51
D6V5, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  N0                           94                            162
  N1                           33                             70
  N2                           28                             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  6(8P11.23) MUTATED   111  16   4   0  23
  AMP PEAK  6(8P11.23) WILD-TYPE 209  36   4   2  27
D6V6, multiclass
     clus
vv    AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  M0                           111                            209
  M1                            16                             36
  M1A                            4                              4
  M1B                            0                              2
  MX                            23                             27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED    75  80
  AMP PEAK  6(8P11.23) WILD-TYPE 132 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED     75   80
  AMP PEAK  6(8P11.23) WILD-TYPE  132  152
        clus
vv       AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  FEMALE                           75                            132
  MALE                             80                            152
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED   139  16
  AMP PEAK  6(8P11.23) WILD-TYPE 239  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED    139   16
  AMP PEAK  6(8P11.23) WILD-TYPE  239   43
                               clus
vv                              AMP PEAK  6(8P11.23) MUTATED
  COLON ADENOCARCINOMA                                   139
  COLON MUCINOUS ADENOCARCINOMA                           16
                               clus
vv                              AMP PEAK  6(8P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                     239
  COLON MUCINOUS ADENOCARCINOMA                             43
[1] 2 2
[1] FALSE
D6V9, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED     2 153
  AMP PEAK  6(8P11.23) WILD-TYPE   1 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED      2  153
  AMP PEAK  6(8P11.23) WILD-TYPE    1  283
     clus
vv    AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  NO                             2                              1
  YES                          153                            283
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(8P11.23) MUTATED   112   1   9  12
  AMP PEAK  6(8P11.23) WILD-TYPE 201   2  15  13
D6V10, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  R0                          112                            201
  R1                            1                              2
  R2                            9                             15
  RX                           12                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  6(8P11.23) MUTATED                                  0     5
  AMP PEAK  6(8P11.23) WILD-TYPE                                1     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(8P11.23) MUTATED                          16    81
  AMP PEAK  6(8P11.23) WILD-TYPE                        34   130
D6V12, multiclass
                                  clus
vv                                 AMP PEAK  6(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      81
                                  clus
vv                                 AMP PEAK  6(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       130
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(8P11.21) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(8P11.21) MUTATED   142  33
  AMP PEAK  7(8P11.21) WILD-TYPE 193  54
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           175                            247 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                            33                             54 
$`AMP PEAK  7(8P11.21) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5657 
       35.11        45.60        13.94        34.65        32.45        31.63 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       32.71        29.16        27.09        25.08        25.18        24.16 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       20.28        61.84         9.63         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3532 
       35.01         6.97         1.02        36.03        19.07        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       29.00        26.01        12.99        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 
       24.00        20.98        19.99        19.99        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       54.02        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 
       37.05        19.00        36.00         5.03        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3869 
        0.99        36.95        17.03        31.07        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3971 TCGA-AA-3975 
       18.05         2.01        12.99        24.00        16.08        34.06 
TCGA-AA-3979 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z 
       24.00        19.00        18.05         0.99        17.03        21.99 
TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02W 
       12.00         1.02        37.02        51.98         0.92        41.00 
TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
        0.07         4.21         1.58         1.02         0.10         0.43 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4615 TCGA-AZ-4616 
        0.92        27.09        21.44         5.19        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6605 
       83.80        22.36        62.79        61.41        49.41         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        3.29         0.07         1.35       102.44        15.62        48.20 
TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       51.32         2.01        20.02        37.02         8.02         8.02 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       27.02        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        15.02        29.03        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5541 
       13.02        11.01        11.08        11.08        10.06        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       20.19         1.32         7.92         4.50        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       13.41        11.38        10.26       119.70        38.20       130.65 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 
        7.50        44.32         6.12        98.24         8.61        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6302 
       13.45         6.18        16.31        16.24         8.35        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 
       53.62        44.68        45.11        39.42        26.43        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       47.15         4.11        10.98        17.29         6.64        30.28 
TCGA-WS-AB45 
       67.00 

$`AMP PEAK  7(8P11.21) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 
       46.65        23.38        42.28        44.91        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       37.25        16.04        36.53        14.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 
       29.19        33.53        23.61        22.09        22.06        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       23.87        20.12        19.66        16.24        24.92        52.44 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
        5.03         1.02         3.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       19.07        34.03         0.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3672 
       23.01        13.94        61.02         6.05         2.01         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       47.05        11.01        85.05        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       14.93         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3947 
       31.07        53.00        17.03        29.98        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 
       21.99        50.99        13.05        26.01        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02         0.99        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       31.00        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        39.06         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        5.03        22.03        39.98        18.05        40.96        21.37 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
       56.55         0.79         0.72         0.76         0.20         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        15.75         0.20        17.82 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
        5.65        65.00         6.77        12.10       100.01        29.56 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 
        3.25         0.26         0.33         0.10        17.56        40.34 
TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       70.16        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6162 
       26.04        13.02        29.06        22.03        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.04        16.04        21.99        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       13.05        11.01        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 
       13.51        20.42        17.75        18.25        15.12        17.85 
TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.49        12.39         9.44        11.64         1.51        12.00 
TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28M 
       81.37       119.93        35.97        60.79       117.07        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 
       13.38        11.11        35.87         1.55        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 
       82.39        23.51        74.56        61.87        55.04        51.75 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        36.00        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        91.79        52.80        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        5.98         5.59         1.32         5.19         5.49        26.99 
TCGA-QG-A5Z2 
       14.76 

  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                        130.65                         140.38 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                         17.03                          21.99 
[1] "0.1 - 130.7 (17.0)" "0.1 - 140.4 (22.0)"
[1] "hr=" "1"  
D7V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  7(8P11.21) MUTATED        33        0       17        50         3
  AMP PEAK  7(8P11.21) WILD-TYPE      39        1       11        81         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(8P11.21) MUTATED           1         9          5         23
  AMP PEAK  7(8P11.21) WILD-TYPE         0        12          7         32
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  7(8P11.21) MUTATED           12       22         7         0
  AMP PEAK  7(8P11.21) WILD-TYPE         26       21        11         2
D7V3, multiclass
            clus
vv           AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  STAGE I                              33                             39
  STAGE IA                              0                              1
  STAGE II                             17                             11
  STAGE IIA                            50                             81
  STAGE IIB                             3                              5
  STAGE IIC                             1                              0
  STAGE III                             9                             12
  STAGE IIIA                            5                              7
  STAGE IIIB                           23                             32
  STAGE IIIC                           12                             26
  STAGE IV                             22                             21
  STAGE IVA                             7                             11
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  7(8P11.21) MUTATED     3  35 127  19
  AMP PEAK  7(8P11.21) WILD-TYPE   8  41 173  32
D7V4, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  T1                            3                              8
  T2                           35                             41
  T3                          127                            173
  T4                           19                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  7(8P11.21) MUTATED   112  39  32
  AMP PEAK  7(8P11.21) WILD-TYPE 144  64  47
D7V5, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  N0                          112                            144
  N1                           39                             64
  N2                           32                             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  7(8P11.21) MUTATED   131  23   6   0  23
  AMP PEAK  7(8P11.21) WILD-TYPE 189  29   2   2  27
D7V6, multiclass
     clus
vv    AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  M0                           131                            189
  M1                            23                             29
  M1A                            6                              2
  M1B                            0                              2
  MX                            23                             27
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED    80 104
  AMP PEAK  7(8P11.21) WILD-TYPE 127 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED     80  104
  AMP PEAK  7(8P11.21) WILD-TYPE  127  128
        clus
vv       AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  FEMALE                           80                            127
  MALE                            104                            128
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED   163  21
  AMP PEAK  7(8P11.21) WILD-TYPE 215  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED    163   21
  AMP PEAK  7(8P11.21) WILD-TYPE  215   38
                               clus
vv                              AMP PEAK  7(8P11.21) MUTATED
  COLON ADENOCARCINOMA                                   163
  COLON MUCINOUS ADENOCARCINOMA                           21
                               clus
vv                              AMP PEAK  7(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                     215
  COLON MUCINOUS ADENOCARCINOMA                             38
[1] 2 2
[1] FALSE
D7V9, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED     2 182
  AMP PEAK  7(8P11.21) WILD-TYPE   1 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED      2  182
  AMP PEAK  7(8P11.21) WILD-TYPE    1  254
     clus
vv    AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  NO                             2                              1
  YES                          182                            254
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  7(8P11.21) MUTATED   132   0  13  13
  AMP PEAK  7(8P11.21) WILD-TYPE 181   3  11  12
D7V10, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  R0                          132                            181
  R1                            0                              3
  R2                           13                             11
  RX                           13                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(8P11.21) MUTATED                                  0     6
  AMP PEAK  7(8P11.21) WILD-TYPE                                1     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(8P11.21) MUTATED                          18    96
  AMP PEAK  7(8P11.21) WILD-TYPE                        32   115
D7V12, multiclass
                                  clus
vv                                 AMP PEAK  7(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  18
  WHITE                                                      96
                                  clus
vv                                 AMP PEAK  7(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    32
  WHITE                                                       115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(8Q12.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(8Q12.1) MUTATED   177  42
  AMP PEAK  8(8Q12.1) WILD-TYPE 158  45
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                          219                           203 
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                           42                            45 
$`AMP PEAK  8(8Q12.1) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 
        5.06         5.26        43.76        43.43        17.79        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 
       45.60        13.94        37.25        16.04        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       32.91        31.63        29.19        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        25.18        24.16        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       20.28         9.63         5.03         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3532 
       35.01         6.97         1.02        36.03        19.07        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       29.00        26.01        12.99        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       24.00        20.98        19.99        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       54.02        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       37.05        36.00         5.03        19.04         0.99         0.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       36.95        37.02        17.03        33.07         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 
       12.99        24.00        34.03         2.01        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K 
       26.01        24.00        27.02        13.94        19.00        18.05 
TCGA-AA-A00L TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A01K 
       17.03         0.99        17.03        21.99        12.00        31.00 
TCGA-AA-A01S TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        1.02        51.98         2.96         5.03         0.92        41.00 
TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 
        0.07         1.58         0.10         0.20         0.43         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       27.09        16.31         0.20        21.44         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       75.25        32.94         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
        0.07         1.35       102.44        15.62        48.20        51.32 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
        2.01        20.02        37.02         8.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 
       29.03        21.99        14.99        12.99        13.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 
       11.08        11.08        10.06        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.19         1.32         7.92        15.12         4.50        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        9.04        13.41        11.38        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F 
      130.65       140.38         7.50        44.32         6.12        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
       60.79       117.07        98.24         8.61        13.38        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 
       13.45         6.18        16.31        16.24         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 
       45.11        39.42        35.93        36.00        26.43        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YX 
       47.15         4.11        10.98         5.98         5.59        17.29 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 
        6.64        30.28        67.00 

$`AMP PEAK  8(8Q12.1) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 
       37.02        46.65        23.38        42.28        44.91        15.52 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       37.05        34.65        14.53        30.44        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 
       22.09        22.06        22.52         8.38        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       24.39        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
       52.44         1.02         3.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       19.07        34.03         0.99        21.01        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 
       23.01        19.99        13.94        61.02         2.01         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 
       47.05        11.01        19.00        85.05        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 
       14.93         0.99        36.03        32.05        31.07        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       31.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 
       21.99        50.99        13.05        25.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N 
       27.02        38.04        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       27.02        42.02        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F 
       33.04        35.01        26.01        37.02        39.06        39.98 
TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 
        2.01        22.03        39.98        18.05        40.96        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         1.02         0.76 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D 
        0.46        14.50         0.95        15.75        17.82         5.52 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-6599 TCGA-AZ-6601 
       50.37        58.39         1.41         5.65         6.77       100.01 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.25         3.29         0.26         0.33         0.10        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       40.34        70.16        21.99        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6170 
       23.05        26.04        22.03        12.00        16.04        15.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       14.04        12.95        13.05        11.01        12.03        14.99 
TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6539 
       19.59        20.42        17.75        18.25        17.85        12.49 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD 
       12.39         9.44        11.64         1.51        12.00        24.43 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB 
       92.75        49.91        13.32        12.59       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 
       95.18        11.11        35.87         1.55        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       82.39        51.75        36.72        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        91.79        52.80        10.52         2.79 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z2 
        1.32         5.19         5.49        26.99        14.76 

  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                         0.07                          0.10 
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                       140.38                        139.17 
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                        17.03                         21.37 
[1] "0.1 - 140.4 (17.0)" "0.1 - 139.2 (21.4)"
[1] "hr=" "1.1"
D8V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  8(8Q12.1) MUTATED        37        0       16        64         3
  AMP PEAK  8(8Q12.1) WILD-TYPE      35        1       12        67         5
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(8Q12.1) MUTATED           1         9          8         31
  AMP PEAK  8(8Q12.1) WILD-TYPE         0        12          4         24
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  8(8Q12.1) MUTATED           20       27        11         0
  AMP PEAK  8(8Q12.1) WILD-TYPE         18       16         7         2
D8V3, multiclass
            clus
vv           AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  STAGE I                             37                            35
  STAGE IA                             0                             1
  STAGE II                            16                            12
  STAGE IIA                           64                            67
  STAGE IIB                            3                             5
  STAGE IIC                            1                             0
  STAGE III                            9                            12
  STAGE IIIA                           8                             4
  STAGE IIIB                          31                            24
  STAGE IIIC                          20                            18
  STAGE IV                            27                            16
  STAGE IVA                           11                             7
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  8(8Q12.1) MUTATED     4  41 160  25
  AMP PEAK  8(8Q12.1) WILD-TYPE   7  35 140  26
D8V4, multiclass
    clus
vv   AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  T1                           4                             7
  T2                          41                            35
  T3                         160                           140
  T4                          25                            26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  8(8Q12.1) MUTATED   130  54  46
  AMP PEAK  8(8Q12.1) WILD-TYPE 126  49  33
D8V5, multiclass
    clus
vv   AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  N0                         130                           126
  N1                          54                            49
  N2                          46                            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                             M0  M1 M1A M1B  MX
  AMP PEAK  8(8Q12.1) MUTATED   161  31   7   0  29
  AMP PEAK  8(8Q12.1) WILD-TYPE 159  21   1   2  21
D8V6, multiclass
     clus
vv    AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  M0                          161                           159
  M1                           31                            21
  M1A                           7                             1
  M1B                           0                             2
  MX                           29                            21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                               cls
clus                              0   1
  AMP PEAK  8(8Q12.1) MUTATED   105 125
  AMP PEAK  8(8Q12.1) WILD-TYPE 102 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q12.1) MUTATED    105  125
  AMP PEAK  8(8Q12.1) WILD-TYPE  102  107
        clus
vv       AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  FEMALE                         105                           102
  MALE                           125                           107
[1] 2 2
[1] FALSE
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(8Q12.1) MUTATED   207  23
  AMP PEAK  8(8Q12.1) WILD-TYPE 171  36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q12.1) MUTATED    207   23
  AMP PEAK  8(8Q12.1) WILD-TYPE  171   36
                               clus
vv                              AMP PEAK  8(8Q12.1) MUTATED
  COLON ADENOCARCINOMA                                  207
  COLON MUCINOUS ADENOCARCINOMA                          23
                               clus
vv                              AMP PEAK  8(8Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    171
  COLON MUCINOUS ADENOCARCINOMA                            36
[1] 2 2
[1] FALSE
D8V9, binary
                               cls
clus                              0   1
  AMP PEAK  8(8Q12.1) MUTATED     3 227
  AMP PEAK  8(8Q12.1) WILD-TYPE   0 209
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q12.1) MUTATED      3  227
  AMP PEAK  8(8Q12.1) WILD-TYPE    0  209
     clus
vv    AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  NO                            3                             0
  YES                         227                           209
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(8Q12.1) MUTATED   160   1  16  14
  AMP PEAK  8(8Q12.1) WILD-TYPE 153   2   8  11
D8V10, multiclass
    clus
vv   AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  R0                         160                           153
  R1                           1                             2
  R2                          16                             8
  RX                          14                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  8(8Q12.1) MUTATED                                  0     5
  AMP PEAK  8(8Q12.1) WILD-TYPE                                1     6
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(8Q12.1) MUTATED                          27   119
  AMP PEAK  8(8Q12.1) WILD-TYPE                        23    92
D8V12, multiclass
                                  clus
vv                                 AMP PEAK  8(8Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 27
  WHITE                                                    119
                                  clus
vv                                 AMP PEAK  8(8Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                       92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(8Q24.21) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(8Q24.21) MUTATED   193  50
  AMP PEAK  9(8Q24.21) WILD-TYPE 142  37
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           243                            179 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                            50                             37 
$`AMP PEAK  9(8Q24.21) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       34.65        36.53        32.45        32.91        31.63        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       23.61        32.71        29.16        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        24.16        20.61        24.69        23.87        20.28 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       52.44         9.63         5.03         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 
       35.01         6.97         1.02        24.03        36.03        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 
       33.99        13.02        24.00        23.01        20.98        19.99 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05         6.97        54.02        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 
       47.01        15.02         5.98        37.05        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 
       85.05        19.04         0.99         0.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03        33.07        36.03         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       24.03        27.02        29.98        18.05         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 
       24.00        20.98        34.03         2.01        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K 
       26.01        24.00        27.02        13.94        19.00        18.05 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
        0.99        17.03        21.99        15.02         0.99        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       31.00         1.02        37.02        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
        5.03         0.92        41.00         0.07        21.37         4.21 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 
        1.58         1.02         0.10         0.20         0.43         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       27.09        16.31         0.20        21.44         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       75.25         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        61.41        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 
        2.14         3.29         0.07         0.10         1.35       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
       15.62        48.20        51.32        21.99         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02         8.02         8.02        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       15.02        17.03        15.02        14.04        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 
       14.99        12.99        13.02        11.08        10.06        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       19.59        13.51        11.51        20.19         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F 
       49.91       140.38         7.50        44.32         6.12        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
       60.79       117.07        98.24         8.61        13.38        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 
       13.45         6.18        16.31        16.24         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        43.07        61.87        53.62        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 
       45.11        39.42        35.93        36.00        26.43        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YX 
       47.15         4.11        10.98         5.59         5.49        17.29 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 
        6.64        30.28        67.00 

$`AMP PEAK  9(8Q24.21) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 TCGA-A6-4105 
       46.65        23.38        42.28        44.91        37.05        14.53 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 
       30.44        33.53        22.09        22.06        22.52         8.38 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       21.76        24.39        20.12        19.66        16.24        24.92 
TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 
       61.84         1.02         3.02        58.03        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
       38.99         1.02         9.07        37.05         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 
       34.03        21.01        17.95        29.95        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3688 
       61.02         2.01         0.92        47.05        11.01        19.00 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3860 
       15.95        38.99        14.93         0.99        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       53.00        31.00        33.01        26.01        24.00         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 
       21.99        50.99        13.05        25.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L 
       27.02        38.04        30.02        34.03        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C 
        4.01        27.02        42.02        14.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       32.02        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02Y 
       35.01        26.01        39.06        39.98        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 
       18.05        40.96        56.55         0.79         0.72         0.76 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D 
        0.46        14.50         0.95        15.75        17.82         5.52 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 
       50.37        58.39         1.41         6.77       100.01         3.25 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5916 
        0.26         0.33        17.56        40.34        70.16        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-6162 
        2.93       124.27        23.05        26.04        22.03        12.00 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       16.04        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6530 TCGA-D5-6531 
       11.08        11.01        12.03        14.99        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       18.25        17.85        12.39         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB 
       12.00        92.75        13.32        12.59       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17        14.04        26.47        81.37       119.93 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 
       95.18        11.11        35.87         1.55        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       82.39        51.75        36.72        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        91.79        52.80        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5Z2 
        5.98         1.32         5.19        26.99        14.76 

  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                          0.07                           0.26 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                        140.38                         139.17 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                         18.05                          21.14 
[1] "0.1 - 140.4 (18.1)" "0.3 - 139.2 (21.1)"
[1] "hr=" "1.1"
D9V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  9(8Q24.21) MUTATED        41        0       18        68         3
  AMP PEAK  9(8Q24.21) WILD-TYPE      31        1       10        63         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(8Q24.21) MUTATED           1        10         10         34
  AMP PEAK  9(8Q24.21) WILD-TYPE         0        11          2         21
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  9(8Q24.21) MUTATED           21       31        13         0
  AMP PEAK  9(8Q24.21) WILD-TYPE         17       12         5         2
D9V3, multiclass
            clus
vv           AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  STAGE I                              41                             31
  STAGE IA                              0                              1
  STAGE II                             18                             10
  STAGE IIA                            68                             63
  STAGE IIB                             3                              5
  STAGE IIC                             1                              0
  STAGE III                            10                             11
  STAGE IIIA                           10                              2
  STAGE IIIB                           34                             21
  STAGE IIIC                           21                             17
  STAGE IV                             31                             12
  STAGE IVA                            13                              5
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  9(8Q24.21) MUTATED     4  47 176  27
  AMP PEAK  9(8Q24.21) WILD-TYPE   7  29 124  24
D9V4, multiclass
    clus
vv   AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  T1                            4                              7
  T2                           47                             29
  T3                          176                            124
  T4                           27                             24
[1] 4 2
[1] 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
  AMP PEAK  9(8Q24.21) MUTATED   144  57  52
  AMP PEAK  9(8Q24.21) WILD-TYPE 112  46  27
D9V5, multiclass
    clus
vv   AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  N0                          144                            112
  N1                           57                             46
  N2                           52                             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                              M0  M1 M1A M1B  MX
  AMP PEAK  9(8Q24.21) MUTATED   178  37   7   0  30
  AMP PEAK  9(8Q24.21) WILD-TYPE 142  15   1   2  20
D9V6, multiclass
     clus
vv    AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  M0                           178                            142
  M1                            37                             15
  M1A                            7                              1
  M1B                            0                              2
  MX                            30                             20
[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"
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED   114 140
  AMP PEAK  9(8Q24.21) WILD-TYPE  93  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED    114  140
  AMP PEAK  9(8Q24.21) WILD-TYPE   93   92
        clus
vv       AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  FEMALE                          114                             93
  MALE                            140                             92
[1] 2 2
[1] FALSE
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED   225  28
  AMP PEAK  9(8Q24.21) WILD-TYPE 153  31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED    225   28
  AMP PEAK  9(8Q24.21) WILD-TYPE  153   31
                               clus
vv                              AMP PEAK  9(8Q24.21) MUTATED
  COLON ADENOCARCINOMA                                   225
  COLON MUCINOUS ADENOCARCINOMA                           28
                               clus
vv                              AMP PEAK  9(8Q24.21) WILD-TYPE
  COLON ADENOCARCINOMA                                     153
  COLON MUCINOUS ADENOCARCINOMA                             31
[1] 2 2
[1] FALSE
D9V9, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED     3 251
  AMP PEAK  9(8Q24.21) WILD-TYPE   0 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED      3  251
  AMP PEAK  9(8Q24.21) WILD-TYPE    0  185
     clus
vv    AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  NO                             3                              0
  YES                          251                            185
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  9(8Q24.21) MUTATED   176   1  17  16
  AMP PEAK  9(8Q24.21) WILD-TYPE 137   2   7   9
D9V10, multiclass
    clus
vv   AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  R0                          176                            137
  R1                            1                              2
  R2                           17                              7
  RX                           16                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  9(8Q24.21) MUTATED                                  0     7
  AMP PEAK  9(8Q24.21) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8Q24.21) MUTATED                          29   130
  AMP PEAK  9(8Q24.21) WILD-TYPE                        21    81
D9V12, multiclass
                                  clus
vv                                 AMP PEAK  9(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  29
  WHITE                                                     130
                                  clus
vv                                 AMP PEAK  9(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    21
  WHITE                                                        81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(11P15.5) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(11P15.5) MUTATED    70  17
  AMP PEAK 10(11P15.5) WILD-TYPE 265  70
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                            87                            335 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                            17                             70 
$`AMP PEAK 10(11P15.5) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-6142 
       37.02        43.43        17.79        44.91        29.19        25.08 
TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3506 
       25.18        23.87         9.63         5.03         1.02        58.03 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3542 
        9.07        24.03        19.07        34.03        29.00        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3673 
       13.02        24.00        23.01        13.94        19.99        50.04 
TCGA-AA-3678 TCGA-AA-3696 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3842 TCGA-AA-3846 
       47.01         5.03        25.02        17.98        37.02        17.03 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3955 TCGA-AA-3982 
       33.07         0.99        24.03        18.05        20.98        27.02 
TCGA-AA-3986 TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01S 
       19.07        34.03        17.03        21.99         0.99         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AD-6888 TCGA-AD-6901 
       35.01        26.01        39.98         5.03         4.21         1.02 
TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 
        0.46        16.31         0.95         6.87        65.00        62.79 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 
       29.56         3.19         1.94         2.14         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6164 
        1.35       102.44         8.02        30.08        17.03        29.03 
TCGA-CM-6166 TCGA-CM-6677 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6536 
       21.99        11.08        12.26        13.51         1.32        17.85 
TCGA-D5-6898 TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6460 
        7.53        13.41        49.91        35.97        60.79        13.38 
TCGA-F4-6463 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
       13.64         8.35        74.56        61.87        55.04        45.11 
TCGA-G4-6314 TCGA-QG-A5YV TCGA-RU-A8FL 
       35.93        26.99        30.28 

$`AMP PEAK 10(11P15.5) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        5.06         5.26        46.65        43.76        23.38        42.28 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       35.11        45.60        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.04        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       24.16        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
        1.02         3.02        37.05         1.02        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3522 
        6.97         1.02        13.02        38.99         1.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3543 
       36.03         8.05        19.07        29.00        26.01         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01         0.92        47.05        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00        36.00        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
       19.04         0.99         0.99        35.05         0.99         1.02 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3854 
       15.95        38.99        36.95        14.93         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       29.98        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00         2.01        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       24.00         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       42.02         0.99        14.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        33.04        37.02        39.06        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 
        1.58         0.10         0.76         0.20         0.43         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
        5.65        32.94         5.13        83.80        22.36        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
        2.24         3.06         3.25         3.29         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02         8.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        15.02        15.02        12.00        14.04        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       14.99        19.59        11.51        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25         7.92        15.12         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.32        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       81.37       119.93       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
       19.43       107.67        28.21        82.39        23.51        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        51.75        39.42        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U 
       91.79        46.75        47.15        52.80         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.52         2.79         5.98         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        17.29         6.64        14.76        67.00 

  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                         19.99                          19.59 
[1] "0.1 - 102.4 (20.0)" "0.1 - 140.4 (19.6)"
[1] "hr=" "1"  
D10V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 10(11P15.5) MUTATED        11        0        4        21         1
  AMP PEAK 10(11P15.5) WILD-TYPE      61        1       24       110         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(11P15.5) MUTATED           0         4          4         14
  AMP PEAK 10(11P15.5) WILD-TYPE         1        17          8         41
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 10(11P15.5) MUTATED           11       12         6         0
  AMP PEAK 10(11P15.5) WILD-TYPE         27       31        12         2
D10V3, multiclass
            clus
vv           AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  STAGE I                              11                             61
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            21                            110
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             4                             17
  STAGE IIIA                            4                              8
  STAGE IIIB                           14                             41
  STAGE IIIC                           11                             27
  STAGE IV                             12                             31
  STAGE IVA                             6                             12
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 10(11P15.5) MUTATED     3  16  66   5
  AMP PEAK 10(11P15.5) WILD-TYPE   8  60 234  46
D10V4, multiclass
    clus
vv   AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  T1                            3                              8
  T2                           16                             60
  T3                           66                            234
  T4                            5                             46
[1] 4 2
[1] 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
  AMP PEAK 10(11P15.5) MUTATED    42  26  21
  AMP PEAK 10(11P15.5) WILD-TYPE 214  77  58
D10V5, multiclass
    clus
vv   AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  N0                           42                            214
  N1                           26                             77
  N2                           21                             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 10(11P15.5) MUTATED    63  15   3   0   7
  AMP PEAK 10(11P15.5) WILD-TYPE 257  37   5   2  43
D10V6, multiclass
     clus
vv    AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  M0                            63                            257
  M1                            15                             37
  M1A                            3                              5
  M1B                            0                              2
  MX                             7                             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"
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED    44  46
  AMP PEAK 10(11P15.5) WILD-TYPE 163 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED     44   46
  AMP PEAK 10(11P15.5) WILD-TYPE  163  186
        clus
vv       AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  FEMALE                           44                            163
  MALE                             46                            186
[1] 2 2
[1] FALSE
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED    85   3
  AMP PEAK 10(11P15.5) WILD-TYPE 293  56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED     85    3
  AMP PEAK 10(11P15.5) WILD-TYPE  293   56
                               clus
vv                              AMP PEAK 10(11P15.5) MUTATED
  COLON ADENOCARCINOMA                                    85
  COLON MUCINOUS ADENOCARCINOMA                            3
                               clus
vv                              AMP PEAK 10(11P15.5) WILD-TYPE
  COLON ADENOCARCINOMA                                     293
  COLON MUCINOUS ADENOCARCINOMA                             56
[1] 2 2
[1] FALSE
D10V9, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED     2  88
  AMP PEAK 10(11P15.5) WILD-TYPE   1 348
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED      2   88
  AMP PEAK 10(11P15.5) WILD-TYPE    1  348
     clus
vv    AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  NO                             2                              1
  YES                           88                            348
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 10(11P15.5) MUTATED    61   1   7   6
  AMP PEAK 10(11P15.5) WILD-TYPE 252   2  17  19
D10V10, multiclass
    clus
vv   AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  R0                           61                            252
  R1                            1                              2
  R2                            7                             17
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(11P15.5) MUTATED                                  0     4
  AMP PEAK 10(11P15.5) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(11P15.5) MUTATED                           6    41
  AMP PEAK 10(11P15.5) WILD-TYPE                        44   170
D10V12, multiclass
                                  clus
vv                                 AMP PEAK 10(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      41
                                  clus
vv                                 AMP PEAK 10(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       170
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(12P13.33) MUTATION ANALYSIS
D11V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 11(12P13.33) MUTATED    78  23
  AMP PEAK 11(12P13.33) WILD-TYPE 257  64
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                            101                             321 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             23                              64 
$`AMP PEAK 11(12P13.33) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3807 
        5.06         5.26        44.91        13.94        16.04        34.65 
TCGA-A6-4105 TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-6782 
       14.53        22.09        25.08        20.61        20.12        20.28 
TCGA-A6-A566 TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3532 TCGA-AA-3534 
       24.92         1.02        58.03        36.03        29.00        29.00 
TCGA-AA-3542 TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3681 
       12.99        19.99        78.08         0.92        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99         0.99        35.05         0.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       37.02        14.93        33.07        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I 
       24.00         2.01        34.03        18.05        12.00        31.00 
TCGA-AA-A01T TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J 
       33.04        51.98         0.92        22.03        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-4323 
        0.07         0.10         0.20         0.92         6.87         1.41 
TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        5.13        49.41         6.77        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6748 
        3.06       102.44        40.34        15.62        51.32         2.01 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 
       20.02         8.02        30.08        16.01        15.02        15.02 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 
       21.99        13.02        14.04        11.01        11.01        20.19 
TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6928 
       17.75         4.50        12.49        15.58        14.30        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D7 
       13.41        12.00        10.26       119.70        24.43        13.32 
TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6703 TCGA-F4-6805 TCGA-G4-6306 
       44.32        95.18         8.61        35.87        16.31        44.68 
TCGA-G4-6314 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A6GB 
       35.93        13.78        47.15        10.98         5.59 

$`AMP PEAK 11(12P13.33) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       37.02        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        35.11        45.60        15.52        37.05        37.25 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        23.61        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       22.52        24.13         8.38        25.18        24.16        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A567 
       24.69        24.39        23.87        19.66        16.24        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       52.44         9.63         5.03         1.02         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        19.07        34.03        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 
       23.01        20.98        13.94        19.99        61.02         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02         2.01        14.01        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
       47.01        15.02        19.00        36.00        85.05        19.04 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       36.95        17.03         0.99        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 
       29.98        18.05        31.00         2.01        33.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E 
        1.02        35.01        26.01        37.02        39.06         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6548 
       39.98         2.01         5.03        41.00        18.05        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.76         0.43         0.46        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
        5.52        75.25        50.37        58.39         5.65        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       83.80        22.36        65.00        62.79        61.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 
      100.01        29.56         5.23         2.24         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4951 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56        70.16        48.20        21.99        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
      124.27        23.05        37.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        15.02         5.03 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       14.99        12.99        15.02        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        20.42        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 
       15.12        17.85        17.13        16.14         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6932 
       10.13        12.43         9.04         9.44         1.51        11.38 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        7.50       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
      117.07        98.24        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18         1.55        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       55.04        51.75        45.11        39.42        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       26.43        22.09        26.04        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        52.80         4.11        10.52         2.79         5.98 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       14.76        30.28        67.00 

  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                         119.70                          140.38 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                          15.62                           21.01 
[1] "0.1 - 119.7 (15.6)" "0.1 - 140.4 (21.0)"
[1] "hr=" "1.4"
D11V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 11(12P13.33) MUTATED        13        1        9        40         2
  AMP PEAK 11(12P13.33) WILD-TYPE      59        0       19        91         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(12P13.33) MUTATED           0         5          5          6
  AMP PEAK 11(12P13.33) WILD-TYPE         1        16          7         49
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 11(12P13.33) MUTATED           10       11         6         0
  AMP PEAK 11(12P13.33) WILD-TYPE         28       32        12         2
D11V3, multiclass
            clus
vv           AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  STAGE I                               13                              59
  STAGE IA                               1                               0
  STAGE II                               9                              19
  STAGE IIA                             40                              91
  STAGE IIB                              2                               6
  STAGE IIC                              0                               1
  STAGE III                              5                              16
  STAGE IIIA                             5                               7
  STAGE IIIB                             6                              49
  STAGE IIIC                            10                              28
  STAGE IV                              11                              32
  STAGE IVA                              6                              12
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 11(12P13.33) MUTATED     0  16  77  16
  AMP PEAK 11(12P13.33) WILD-TYPE  11  60 223  35
D11V4, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  T1                             0                              11
  T2                            16                              60
  T3                            77                             223
  T4                            16                              35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 11(12P13.33) MUTATED    69  20  21
  AMP PEAK 11(12P13.33) WILD-TYPE 187  83  58
D11V5, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  N0                            69                             187
  N1                            20                              83
  N2                            21                              58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 11(12P13.33) MUTATED    78  12   5   0  14
  AMP PEAK 11(12P13.33) WILD-TYPE 242  40   3   2  36
D11V6, multiclass
     clus
vv    AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  M0                             78                             242
  M1                             12                              40
  M1A                             5                               3
  M1B                             0                               2
  MX                             14                              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"
D11V7, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED    53  57
  AMP PEAK 11(12P13.33) WILD-TYPE 154 175
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     53   57
  AMP PEAK 11(12P13.33) WILD-TYPE  154  175
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  FEMALE                            53                             154
  MALE                              57                             175
[1] 2 2
[1] FALSE
D11V8, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED    96  14
  AMP PEAK 11(12P13.33) WILD-TYPE 282  45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     96   14
  AMP PEAK 11(12P13.33) WILD-TYPE  282   45
                               clus
vv                              AMP PEAK 11(12P13.33) MUTATED
  COLON ADENOCARCINOMA                                     96
  COLON MUCINOUS ADENOCARCINOMA                            14
                               clus
vv                              AMP PEAK 11(12P13.33) WILD-TYPE
  COLON ADENOCARCINOMA                                      282
  COLON MUCINOUS ADENOCARCINOMA                              45
[1] 2 2
[1] FALSE
D11V9, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED     0 110
  AMP PEAK 11(12P13.33) WILD-TYPE   3 326
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED      0  110
  AMP PEAK 11(12P13.33) WILD-TYPE    3  326
     clus
vv    AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  NO                              0                               3
  YES                           110                             326
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 11(12P13.33) MUTATED    81   1   3   5
  AMP PEAK 11(12P13.33) WILD-TYPE 232   2  21  20
D11V10, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  R0                            81                             232
  R1                             1                               2
  R2                             3                              21
  RX                             5                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(12P13.33) MUTATED                                  0     1
  AMP PEAK 11(12P13.33) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(12P13.33) MUTATED                          11    55
  AMP PEAK 11(12P13.33) WILD-TYPE                        39   156
D11V12, multiclass
                                  clus
vv                                 AMP PEAK 11(12P13.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                       55
                                  clus
vv                                 AMP PEAK 11(12P13.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     39
  WHITE                                                        156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(13Q12.13) MUTATION ANALYSIS
D12V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 12(13Q12.13) MUTATED   205  54
  AMP PEAK 12(13Q12.13) WILD-TYPE 130  33
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            259                             163 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                             54                              33 
$`AMP PEAK 12(13Q12.13) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       29.19        33.53        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        24.13        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.69        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        9.63         5.03         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 
        6.97        38.99         9.07        24.03        36.03        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 
       13.94        19.99        78.08         6.05         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 
       50.04        15.02         5.98        37.05        19.00         5.03 
TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       85.05         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 
       36.95        37.02        14.93        17.03         0.99        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       29.98         2.01        12.99        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       26.01        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W 
       13.94        19.00        34.03        17.03        42.02        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y 
       33.04         2.96        39.98         2.01        41.00        39.98 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       40.96        21.37         0.79         1.58         1.02         0.10 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.20         0.43        14.50        16.31         0.95        15.75 
TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 
       21.44         5.19         6.87        75.25        50.37         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13        83.80        22.36        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 
        3.06         0.07         1.35        17.56       102.44        48.20 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       21.99         2.01        20.02         8.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        14.04        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 
       14.99        12.99        13.02        15.02        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        11.01        10.06        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       11.51        17.75        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.50        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70       130.65        92.75        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
        7.50       131.51         7.76         6.12        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 
      119.93        35.97         8.61        13.38         6.18        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 
       16.24        33.67         1.28         0.53        35.41       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 
       44.68        45.11        39.42        35.93        36.00        26.43 
TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       35.80        91.79        46.75        47.15         4.11        10.52 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         5.19         5.49        26.99        17.29         6.64 
TCGA-RU-A8FL 
       30.28 

$`AMP PEAK 12(13Q12.13) WILD-TYPE`
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       23.38        17.79        37.05        37.25        16.04        31.63 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02        13.02         1.02        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 TCGA-AA-3663 
       19.07        17.95        29.95        23.01        61.02         6.97 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 
       54.02         0.92        47.05        47.01        11.01        36.00 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       26.99        19.04         1.02        17.98        15.95        38.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 
       33.07        36.03        53.00        18.05        31.00        33.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E 
       24.00         2.01         2.01        25.02        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       21.99        34.98        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6888 
        5.03         0.92        22.03        18.05         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       56.55         0.72         0.76         0.46         0.92        27.09 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
        0.20        17.82         5.52        58.39         5.65        32.94 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 
       61.41         6.77       100.01         3.19         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 
        3.29         0.26         0.33         0.10        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14         2.93       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 
       37.02        26.04        27.02        15.02        15.02        12.00 
TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 
       21.99        14.04        12.95        13.05        12.03        14.99 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       20.19        20.42        16.14        15.58        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.64         1.51        24.43        38.20        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H 
       44.32       135.65       139.17        81.37        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 
       98.24        95.18        11.11        13.64        13.45        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 
        1.55        16.31        19.43        43.07        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 
       51.75        36.72        22.09        26.04        13.78        26.17 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z2 
       52.80        10.98         2.79         5.98         1.32        14.76 
TCGA-WS-AB45 
       67.00 

  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                         131.51                          140.38 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                          19.07                           20.12 
[1] "0.1 - 131.5 (19.1)" "0.1 - 140.4 (20.1)"
[1] "hr=" "1.1"
D12V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 12(13Q12.13) MUTATED        42        0       14        68         2
  AMP PEAK 12(13Q12.13) WILD-TYPE      30        1       14        63         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(13Q12.13) MUTATED           1        11         11         38
  AMP PEAK 12(13Q12.13) WILD-TYPE         0        10          1         17
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(13Q12.13) MUTATED           24       36        15         0
  AMP PEAK 12(13Q12.13) WILD-TYPE         14        7         3         2
D12V3, multiclass
            clus
vv           AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  STAGE I                               42                              30
  STAGE IA                               0                               1
  STAGE II                              14                              14
  STAGE IIA                             68                              63
  STAGE IIB                              2                               6
  STAGE IIC                              1                               0
  STAGE III                             11                              10
  STAGE IIIA                            11                               1
  STAGE IIIB                            38                              17
  STAGE IIIC                            24                              14
  STAGE IV                              36                               7
  STAGE IVA                             15                               3
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 12(13Q12.13) MUTATED     7  45 186  29
  AMP PEAK 12(13Q12.13) WILD-TYPE   4  31 114  22
D12V4, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  T1                             7                               4
  T2                            45                              31
  T3                           186                             114
  T4                            29                              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 12(13Q12.13) MUTATED   137  75  55
  AMP PEAK 12(13Q12.13) WILD-TYPE 119  28  24
D12V5, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  N0                           137                             119
  N1                            75                              28
  N2                            55                              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                               M0  M1 M1A M1B  MX
  AMP PEAK 12(13Q12.13) MUTATED   185  43   7   0  29
  AMP PEAK 12(13Q12.13) WILD-TYPE 135   9   1   2  21
D12V6, multiclass
     clus
vv    AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  M0                            185                             135
  M1                             43                               9
  M1A                             7                               1
  M1B                             0                               2
  MX                             29                              21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED   124 143
  AMP PEAK 12(13Q12.13) WILD-TYPE  83  89
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED    124  143
  AMP PEAK 12(13Q12.13) WILD-TYPE   83   89
        clus
vv       AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  FEMALE                           124                              83
  MALE                             143                              89
[1] 2 2
[1] FALSE
D12V8, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED   249  17
  AMP PEAK 12(13Q12.13) WILD-TYPE 129  42
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED    249   17
  AMP PEAK 12(13Q12.13) WILD-TYPE  129   42
                               clus
vv                              AMP PEAK 12(13Q12.13) MUTATED
  COLON ADENOCARCINOMA                                    249
  COLON MUCINOUS ADENOCARCINOMA                            17
                               clus
vv                              AMP PEAK 12(13Q12.13) WILD-TYPE
  COLON ADENOCARCINOMA                                      129
  COLON MUCINOUS ADENOCARCINOMA                              42
[1] 2 2
[1] FALSE
D12V9, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED     3 264
  AMP PEAK 12(13Q12.13) WILD-TYPE   0 172
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED      3  264
  AMP PEAK 12(13Q12.13) WILD-TYPE    0  172
     clus
vv    AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  NO                              3                               0
  YES                           264                             172
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 12(13Q12.13) MUTATED   189   1  19  10
  AMP PEAK 12(13Q12.13) WILD-TYPE 124   2   5  15
D12V10, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  R0                           189                             124
  R1                             1                               2
  R2                            19                               5
  RX                            10                              15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(13Q12.13) MUTATED                                  0     4
  AMP PEAK 12(13Q12.13) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(13Q12.13) MUTATED                          30   135
  AMP PEAK 12(13Q12.13) WILD-TYPE                        20    76
D12V12, multiclass
                                  clus
vv                                 AMP PEAK 12(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   30
  WHITE                                                      135
                                  clus
vv                                 AMP PEAK 12(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     20
  WHITE                                                         76
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(13Q22.1) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(13Q22.1) MUTATED   208  55
  AMP PEAK 13(13Q22.1) WILD-TYPE 127  32
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                           263                            159 
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                            55                             32 
$`AMP PEAK 13(13Q22.1) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       29.19        33.53        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        24.13        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.69        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        9.63         5.03         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 
        6.97        38.99         9.07        24.03        36.03        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       21.01        13.02        24.00        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       19.99        78.08         6.05        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 
       50.04        15.02         5.98        37.05        19.00        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 
        0.99         0.99        35.05         0.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       14.93        17.03         0.99        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 
       17.03        24.03        27.02        29.98        18.05         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       12.99        24.00        26.01         2.01        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       34.03        17.03        42.02        17.03        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01S 
       15.02         0.99        32.02        12.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y 
       33.04         2.96        39.98         2.01        41.00        39.98 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37         4.21         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        1.58         1.02         0.10         0.20         0.43        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       16.31         0.95        15.75        21.44         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       75.25        50.37         1.41         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
        1.94         2.24         3.06         0.07         1.35        17.56 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 
      102.44        48.20        21.99         2.01        20.02         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
       16.01         5.03        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 
       11.01        11.08        11.08        11.01        10.06        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        7.92        15.12        17.85         4.50        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        92.75        49.91        13.32         7.50       131.51 
TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
        7.76         6.12        14.04        26.47       119.93        35.97 
TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       13.38         6.18        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        0.53        35.41       107.67        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 
       23.51        74.56        61.87        44.68        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       35.93        36.00        26.43        35.80        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       47.15         4.11        10.52         5.98         5.59         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        30.28 

$`AMP PEAK 13(13Q22.1) WILD-TYPE`
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       23.38        17.79        37.05        37.25        16.04        31.63 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.09        22.06         8.38        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 TCGA-AA-3510 
       16.24        24.92         3.02         1.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02        13.02         1.02        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3655 
       19.07        33.99        17.95        29.95        23.01        61.02 
TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3692 
        6.97         0.92        47.05        47.01        11.01        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        5.03        26.99        19.04        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 
       15.95        38.99        33.07        36.03        31.07        53.00 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3979 
       31.00        33.01        24.00         2.01        25.02        24.00 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        21.99        34.98        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 
        5.03         0.92        22.03        18.05        56.55         0.76 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D 
        0.46         0.92        27.09         0.20        17.82         5.52 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5407 TCGA-AZ-6599 
       58.39         5.65        32.94        83.80        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
      100.01         3.19         2.14         3.25         3.29         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.33         0.10        40.34        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
       21.14         2.93       124.27        23.05        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 
       27.02        15.02        15.02        12.00        21.99        14.04 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 
       12.95        13.05        12.03        14.99        20.19        20.42 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       16.14        15.58        12.39         9.44        11.64         1.51 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C 
       12.59       140.38        44.32       135.65       139.17        81.37 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 
       13.64        13.45        35.87         1.55        16.31        19.43 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
       43.07        53.62        55.04        51.75        36.72        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV 
       26.04        13.78        26.17        52.80        10.98         2.79 
TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 
        1.32        14.76        67.00 

  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                        131.51                         140.38 
  AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE 
                         18.05                          21.99 
[1] "0.1 - 131.5 (18.1)" "0.1 - 140.4 (22.0)"
[1] "hr=" "1.2"
D13V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 13(13Q22.1) MUTATED        44        0       15        66         2
  AMP PEAK 13(13Q22.1) WILD-TYPE      28        1       13        65         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(13Q22.1) MUTATED           1        12         11         38
  AMP PEAK 13(13Q22.1) WILD-TYPE         0         9          1         17
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(13Q22.1) MUTATED           26       35        15         0
  AMP PEAK 13(13Q22.1) WILD-TYPE         12        8         3         2
D13V3, multiclass
            clus
vv           AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  STAGE I                              44                             28
  STAGE IA                              0                              1
  STAGE II                             15                             13
  STAGE IIA                            66                             65
  STAGE IIB                             2                              6
  STAGE IIC                             1                              0
  STAGE III                            12                              9
  STAGE IIIA                           11                              1
  STAGE IIIB                           38                             17
  STAGE IIIC                           26                             12
  STAGE IV                             35                              8
  STAGE IVA                            15                              3
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 13(13Q22.1) MUTATED     8  47 186  30
  AMP PEAK 13(13Q22.1) WILD-TYPE   3  29 114  21
D13V4, multiclass
    clus
vv   AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  T1                            8                              3
  T2                           47                             29
  T3                          186                            114
  T4                           30                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 13(13Q22.1) MUTATED   138  76  56
  AMP PEAK 13(13Q22.1) WILD-TYPE 118  27  23
D13V5, multiclass
    clus
vv   AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  N0                          138                            118
  N1                           76                             27
  N2                           56                             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                              M0  M1 M1A M1B  MX
  AMP PEAK 13(13Q22.1) MUTATED   187  42   7   0  32
  AMP PEAK 13(13Q22.1) WILD-TYPE 133  10   1   2  18
D13V6, multiclass
     clus
vv    AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  M0                           187                            133
  M1                            42                             10
  M1A                            7                              1
  M1B                            0                              2
  MX                            32                             18
[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"
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q22.1) MUTATED   122 149
  AMP PEAK 13(13Q22.1) WILD-TYPE  85  83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q22.1) MUTATED    122  149
  AMP PEAK 13(13Q22.1) WILD-TYPE   85   83
        clus
vv       AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  FEMALE                          122                             85
  MALE                            149                             83
[1] 2 2
[1] FALSE
D13V8, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q22.1) MUTATED   251  19
  AMP PEAK 13(13Q22.1) WILD-TYPE 127  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q22.1) MUTATED    251   19
  AMP PEAK 13(13Q22.1) WILD-TYPE  127   40
                               clus
vv                              AMP PEAK 13(13Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   251
  COLON MUCINOUS ADENOCARCINOMA                           19
                               clus
vv                              AMP PEAK 13(13Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     127
  COLON MUCINOUS ADENOCARCINOMA                             40
[1] 2 2
[1] FALSE
D13V9, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q22.1) MUTATED     3 268
  AMP PEAK 13(13Q22.1) WILD-TYPE   0 168
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q22.1) MUTATED      3  268
  AMP PEAK 13(13Q22.1) WILD-TYPE    0  168
     clus
vv    AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  NO                             3                              0
  YES                          268                            168
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(13Q22.1) MUTATED   191   1  18  10
  AMP PEAK 13(13Q22.1) WILD-TYPE 122   2   6  15
D13V10, multiclass
    clus
vv   AMP PEAK 13(13Q22.1) MUTATED AMP PEAK 13(13Q22.1) WILD-TYPE
  R0                          191                            122
  R1                            1                              2
  R2                           18                              6
  RX                           10                             15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(13Q22.1) MUTATED                                  0     4
  AMP PEAK 13(13Q22.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(13Q22.1) MUTATED                          31   138
  AMP PEAK 13(13Q22.1) WILD-TYPE                        19    73
D13V12, multiclass
                                  clus
vv                                 AMP PEAK 13(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  31
  WHITE                                                     138
                                  clus
vv                                 AMP PEAK 13(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                        73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(16P11.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(16P11.2) MUTATED    96  20
  AMP PEAK 14(16P11.2) WILD-TYPE 239  67
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                           116                            306 
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                            20                             67 
$`AMP PEAK 14(16P11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       37.02        43.43        17.79        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       15.52        37.25        32.45        30.44        29.19        29.16 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 
       24.13        25.08        20.61        23.87        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 
       12.99        33.99        13.02        24.00        19.99        19.99 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3812 TCGA-AA-3841 TCGA-AA-3842 
       50.04        15.02        19.00        35.05        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 
       14.93        17.03        33.07         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       24.03        27.02        29.98         2.01        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3982 
        2.01        20.98        34.03        16.08        26.01        27.02 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A02W 
       34.03        42.02        15.02        12.00        33.04        41.00 
TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-5543 
       40.96         1.02         0.10         0.20         0.95        15.75 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 
        0.20         5.19         6.87         5.13        62.79        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 
        5.23         1.94         2.24         3.29         1.35       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 
       48.20        21.99        20.02         8.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       22.98        16.01        17.03        14.04        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 
       14.99        15.02        11.01        10.06        19.59        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6929 
        1.32        15.12        17.13        12.49        10.13        13.41 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 
       11.38        38.20        13.32        35.97         8.61        13.38 
TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
        1.55        82.39        74.56        61.87        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 
       45.11        39.42        35.93        26.43        13.78        46.75 
TCGA-NH-A6GB TCGA-NH-A6GC 
        5.59         1.32 

$`AMP PEAK 14(16P11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 
        5.06         5.26        46.65        43.76        23.38        42.28 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       13.94        37.05        16.04        34.65        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 
       19.07        19.07        34.03        29.00         0.99        14.01 
TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 
       21.01        17.95        29.95        23.01        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.05        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99         0.99         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       15.95        38.99         0.99        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       53.00        18.05        31.00        33.01        26.01        24.00 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        50.99        13.05        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         1.58         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.43         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.52        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94        83.80        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        3.19         3.06         2.14         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5349 
       37.02         8.02        26.04        27.02        29.06        30.08 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       16.04        12.99        13.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        12.03        14.99        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 
       13.51        11.51        20.19        20.42        17.75         7.92 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.50        16.14        15.58         7.53        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        12.59       140.38         7.50        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        60.79       117.07        98.24        95.18 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        13.64        13.45         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 
       19.43       107.67        28.21         8.35        23.51        43.07 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 
       53.62        51.75        36.72        36.00        22.09        26.04 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        91.79        47.15        52.80         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.98        10.52         2.79         5.98         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 

  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE 
                        20.315                         19.070 
[1] "0.1 - 102.4 (20.3)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.2"
D14V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 14(16P11.2) MUTATED        13        1        3        29         1
  AMP PEAK 14(16P11.2) WILD-TYPE      59        0       25       102         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(16P11.2) MUTATED           0         5          9         20
  AMP PEAK 14(16P11.2) WILD-TYPE         1        16          3         35
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 14(16P11.2) MUTATED           16       15         5         1
  AMP PEAK 14(16P11.2) WILD-TYPE         22       28        13         1
D14V3, multiclass
            clus
vv           AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  STAGE I                              13                             59
  STAGE IA                              1                              0
  STAGE II                              3                             25
  STAGE IIA                            29                            102
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             5                             16
  STAGE IIIA                            9                              3
  STAGE IIIB                           20                             35
  STAGE IIIC                           16                             22
  STAGE IV                             15                             28
  STAGE IVA                             5                             13
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 14(16P11.2) MUTATED     3  18  89  11
  AMP PEAK 14(16P11.2) WILD-TYPE   8  58 211  40
D14V4, multiclass
    clus
vv   AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  T1                            3                              8
  T2                           18                             58
  T3                           89                            211
  T4                           11                             40
[1] 4 2
[1] 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
  AMP PEAK 14(16P11.2) MUTATED    52  37  33
  AMP PEAK 14(16P11.2) WILD-TYPE 204  66  46
D14V5, multiclass
    clus
vv   AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  N0                           52                            204
  N1                           37                             66
  N2                           33                             46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 14(16P11.2) MUTATED    83  17   3   1  15
  AMP PEAK 14(16P11.2) WILD-TYPE 237  35   5   1  35
D14V6, multiclass
     clus
vv    AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  M0                            83                            237
  M1                            17                             35
  M1A                            3                              5
  M1B                            1                              1
  MX                            15                             35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(16P11.2) MUTATED    60  62
  AMP PEAK 14(16P11.2) WILD-TYPE 147 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16P11.2) MUTATED     60   62
  AMP PEAK 14(16P11.2) WILD-TYPE  147  170
        clus
vv       AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  FEMALE                           60                            147
  MALE                             62                            170
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(16P11.2) MUTATED   113   8
  AMP PEAK 14(16P11.2) WILD-TYPE 265  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16P11.2) MUTATED    113    8
  AMP PEAK 14(16P11.2) WILD-TYPE  265   51
                               clus
vv                              AMP PEAK 14(16P11.2) MUTATED
  COLON ADENOCARCINOMA                                   113
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              AMP PEAK 14(16P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     265
  COLON MUCINOUS ADENOCARCINOMA                             51
[1] 2 2
[1] FALSE
D14V9, binary
                                cls
clus                               0   1
  AMP PEAK 14(16P11.2) MUTATED     1 121
  AMP PEAK 14(16P11.2) WILD-TYPE   2 315
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(16P11.2) MUTATED      1  121
  AMP PEAK 14(16P11.2) WILD-TYPE    2  315
     clus
vv    AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  NO                             1                              2
  YES                          121                            315
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(16P11.2) MUTATED    93   0   7   5
  AMP PEAK 14(16P11.2) WILD-TYPE 220   3  17  20
D14V10, multiclass
    clus
vv   AMP PEAK 14(16P11.2) MUTATED AMP PEAK 14(16P11.2) WILD-TYPE
  R0                           93                            220
  R1                            0                              3
  R2                            7                             17
  RX                            5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(16P11.2) MUTATED                                  1     3
  AMP PEAK 14(16P11.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(16P11.2) MUTATED                          12    61
  AMP PEAK 14(16P11.2) WILD-TYPE                        38   150
D14V12, multiclass
                                  clus
vv                                 AMP PEAK 14(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      61
                                  clus
vv                                 AMP PEAK 14(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    38
  WHITE                                                       150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = AMP PEAK 15(16Q12.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(16Q12.1) MUTATED    89  14
  AMP PEAK 15(16Q12.1) WILD-TYPE 246  73
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                           103                            319 
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                            14                             73 
$`AMP PEAK 15(16Q12.1) MUTATED`
TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       43.43        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       15.52        37.25        32.45        30.44        29.19        29.16 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       24.13        25.08        23.87        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3673 
       33.99        13.02        24.00        19.99        19.99        50.04 
TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.02        19.00        36.95        37.02        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3939 
       33.07         0.99        17.03        24.03        27.02        12.99 
TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3982 
       24.00        20.98        34.03        16.08        26.01        27.02 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A02W 
       34.03        42.02        15.02        12.00        33.04        41.00 
TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 TCGA-AY-6196 
       40.96         1.02         0.10         0.20         0.95         0.20 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 
        5.19         6.87         5.13        62.79        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 
        1.94         3.29         1.35       102.44        48.20        21.99 
TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5868 
       20.02         8.02        22.03        22.98        16.01        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6170 TCGA-CM-6172 
       14.04        29.03        21.99        14.99        15.02        11.01 
TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 
       10.06        19.59        18.25         1.32        15.12        17.13 
TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A28F 
       12.49        10.13        13.41        11.38        38.20        35.97 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-G4-6297 TCGA-G4-6306 TCGA-G4-6307 
        8.61        13.38         1.55        82.39        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6323 TCGA-NH-A6GB 
       45.11        39.42        35.93        26.43        13.78         5.59 
TCGA-NH-A6GC 
        1.32 

$`AMP PEAK 15(16Q12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.76        23.38 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       13.94        37.05        16.04        34.65        36.53        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       32.71        27.09        22.52         8.38        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3543 
        8.05        19.07        19.07        34.03        29.00         0.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       14.01        21.01        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
        2.01        14.01         0.92        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3848 TCGA-AA-3854 
        1.02        17.98        15.95        38.99         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3875 
       32.05        31.07        31.07        53.00        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        50.99        13.05        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        32.02        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         1.58         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.43         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 
       15.75        21.44        17.82         5.52        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 
        0.07         0.26         0.33         0.10        17.56        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        15.62        51.32        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        37.02         8.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       13.02        29.06        30.08        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       15.02        15.02        12.00        16.04        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        14.99        12.26        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75         7.92        17.85         4.50        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        12.39        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24        95.18        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       28.21         8.35        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 
       53.62        51.75        36.72        36.00        22.09        26.04 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F7 
        4.11        10.98        10.52         2.79         5.98         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 
       67.00 

  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE 
                         20.02                          19.07 
[1] "0.1 - 102.4 (20.0)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.5"
D15V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 15(16Q12.1) MUTATED        13        1        3        22         1
  AMP PEAK 15(16Q12.1) WILD-TYPE      59        0       25       109         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(16Q12.1) MUTATED           0         5          9         20
  AMP PEAK 15(16Q12.1) WILD-TYPE         1        16          3         35
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 15(16Q12.1) MUTATED           14       11         4         1
  AMP PEAK 15(16Q12.1) WILD-TYPE         24       32        14         1
D15V3, multiclass
            clus
vv           AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  STAGE I                              13                             59
  STAGE IA                              1                              0
  STAGE II                              3                             25
  STAGE IIA                            22                            109
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             5                             16
  STAGE IIIA                            9                              3
  STAGE IIIB                           20                             35
  STAGE IIIC                           14                             24
  STAGE IV                             11                             32
  STAGE IVA                             4                             14
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 15(16Q12.1) MUTATED     3  18  75  11
  AMP PEAK 15(16Q12.1) WILD-TYPE   8  58 225  40
D15V4, multiclass
    clus
vv   AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  T1                            3                              8
  T2                           18                             58
  T3                           75                            225
  T4                           11                             40
[1] 4 2
[1] 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
  AMP PEAK 15(16Q12.1) MUTATED    45  35  28
  AMP PEAK 15(16Q12.1) WILD-TYPE 211  68  51
D15V5, multiclass
    clus
vv   AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  N0                           45                            211
  N1                           35                             68
  N2                           28                             51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 15(16Q12.1) MUTATED    74  12   3   1  15
  AMP PEAK 15(16Q12.1) WILD-TYPE 246  40   5   1  35
D15V6, multiclass
     clus
vv    AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  M0                            74                            246
  M1                            12                             40
  M1A                            3                              5
  M1B                            1                              1
  MX                            15                             35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(16Q12.1) MUTATED    54  54
  AMP PEAK 15(16Q12.1) WILD-TYPE 153 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16Q12.1) MUTATED     54   54
  AMP PEAK 15(16Q12.1) WILD-TYPE  153  178
        clus
vv       AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  FEMALE                           54                            153
  MALE                             54                            178
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(16Q12.1) MUTATED   100   7
  AMP PEAK 15(16Q12.1) WILD-TYPE 278  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16Q12.1) MUTATED    100    7
  AMP PEAK 15(16Q12.1) WILD-TYPE  278   52
                               clus
vv                              AMP PEAK 15(16Q12.1) MUTATED
  COLON ADENOCARCINOMA                                   100
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              AMP PEAK 15(16Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     278
  COLON MUCINOUS ADENOCARCINOMA                             52
[1] 2 2
[1] FALSE
D15V9, binary
                                cls
clus                               0   1
  AMP PEAK 15(16Q12.1) MUTATED     1 107
  AMP PEAK 15(16Q12.1) WILD-TYPE   2 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16Q12.1) MUTATED      1  107
  AMP PEAK 15(16Q12.1) WILD-TYPE    2  329
     clus
vv    AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  NO                             1                              2
  YES                          107                            329
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(16Q12.1) MUTATED    83   0   6   4
  AMP PEAK 15(16Q12.1) WILD-TYPE 230   3  18  21
D15V10, multiclass
    clus
vv   AMP PEAK 15(16Q12.1) MUTATED AMP PEAK 15(16Q12.1) WILD-TYPE
  R0                           83                            230
  R1                            0                              3
  R2                            6                             18
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(16Q12.1) MUTATED                                  1     2
  AMP PEAK 15(16Q12.1) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(16Q12.1) MUTATED                           9    57
  AMP PEAK 15(16Q12.1) WILD-TYPE                        41   154
D15V12, multiclass
                                  clus
vv                                 AMP PEAK 15(16Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      57
                                  clus
vv                                 AMP PEAK 15(16Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(17P11.2) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(17P11.2) MUTATED    34   7
  AMP PEAK 16(17P11.2) WILD-TYPE 301  80
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                            41                            381 
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                             7                             80 
$`AMP PEAK 16(17P11.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2680 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5657 
        5.06         5.26        35.11        16.04        36.53        31.63 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-A56B TCGA-AA-3679 
       30.44        32.71        29.16        25.08        52.44        15.02 
TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3939 
       35.05         1.02        36.95        17.03         0.99        12.99 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3975 TCGA-AD-6888 TCGA-AZ-5407 
       34.03         2.01        13.05        34.06         4.21        61.41 
TCGA-AZ-6607 TCGA-CA-6719 TCGA-CM-5341 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-6537 
        3.19         1.35        29.06        14.04        11.01         4.50 
TCGA-D5-6924 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6704 
       14.30         6.12        14.04       119.93        95.18         1.55 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6317 
       23.51        74.56        55.04        35.93        36.00 

$`AMP PEAK 16(17P11.2) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
       37.02        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        44.91        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5660 
       37.25        34.65        14.53        32.45        32.91        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 
       33.53        23.61        22.09        22.06        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        61.84         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 
       85.05        26.99        19.04         0.99         0.99         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       25.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 
        0.99        33.07        36.03        32.05        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3976 
        2.01        20.98        21.99        16.08        50.99        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
        0.99        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       37.02        39.06        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        5.03         0.92        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        1.58         1.02         0.10         0.76         0.20         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.29         0.07         0.26         0.33         0.10        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02         8.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       13.02        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
        1.32         7.92        15.12        17.85        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A 
       44.32       131.51       135.65         7.76       139.17        26.47 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       35.41        19.43       107.67        28.21         8.35        82.39 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 
       43.07        61.87        53.62        44.68        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       14.76        30.28        67.00 

  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                          0.99                           0.07 
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                        119.93                         140.38 
  AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE 
                         23.51                          19.59 
[1] "1.0 - 119.9 (23.5)" "0.1 - 140.4 (19.6)"
[1] "hr=" "1.3"
D16V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 16(17P11.2) MUTATED         6        0        1        15         0
  AMP PEAK 16(17P11.2) WILD-TYPE      66        1       27       116         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(17P11.2) MUTATED           1         1          1          7
  AMP PEAK 16(17P11.2) WILD-TYPE         0        20         11         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 16(17P11.2) MUTATED            4        5         2         0
  AMP PEAK 16(17P11.2) WILD-TYPE         34       38        16         2
D16V3, multiclass
            clus
vv           AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  STAGE I                               6                             66
  STAGE IA                              0                              1
  STAGE II                              1                             27
  STAGE IIA                            15                            116
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             1                             20
  STAGE IIIA                            1                             11
  STAGE IIIB                            7                             48
  STAGE IIIC                            4                             34
  STAGE IV                              5                             38
  STAGE IVA                             2                             16
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 16(17P11.2) MUTATED     2   6  30   5
  AMP PEAK 16(17P11.2) WILD-TYPE   9  70 270  46
D16V4, multiclass
    clus
vv   AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  T1                            2                              9
  T2                            6                             70
  T3                           30                            270
  T4                            5                             46
[1] 4 2
[1] 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
  AMP PEAK 16(17P11.2) MUTATED    23  10   9
  AMP PEAK 16(17P11.2) WILD-TYPE 233  93  70
D16V5, multiclass
    clus
vv   AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  N0                           23                            233
  N1                           10                             93
  N2                            9                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 16(17P11.2) MUTATED    30   5   2   0   6
  AMP PEAK 16(17P11.2) WILD-TYPE 290  47   6   2  44
D16V6, multiclass
     clus
vv    AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  M0                            30                            290
  M1                             5                             47
  M1A                            2                              6
  M1B                            0                              2
  MX                             6                             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"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(17P11.2) MUTATED    19  24
  AMP PEAK 16(17P11.2) WILD-TYPE 188 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17P11.2) MUTATED     19   24
  AMP PEAK 16(17P11.2) WILD-TYPE  188  208
        clus
vv       AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  FEMALE                           19                            188
  MALE                             24                            208
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(17P11.2) MUTATED    37   6
  AMP PEAK 16(17P11.2) WILD-TYPE 341  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17P11.2) MUTATED     37    6
  AMP PEAK 16(17P11.2) WILD-TYPE  341   53
                               clus
vv                              AMP PEAK 16(17P11.2) MUTATED
  COLON ADENOCARCINOMA                                    37
  COLON MUCINOUS ADENOCARCINOMA                            6
                               clus
vv                              AMP PEAK 16(17P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     341
  COLON MUCINOUS ADENOCARCINOMA                             53
[1] 2 2
[1] FALSE
D16V9, binary
                                cls
clus                               0   1
  AMP PEAK 16(17P11.2) MUTATED     0  43
  AMP PEAK 16(17P11.2) WILD-TYPE   3 393
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(17P11.2) MUTATED      0   43
  AMP PEAK 16(17P11.2) WILD-TYPE    3  393
     clus
vv    AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  NO                             0                              3
  YES                           43                            393
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(17P11.2) MUTATED    31   0   2   1
  AMP PEAK 16(17P11.2) WILD-TYPE 282   3  22  24
D16V10, multiclass
    clus
vv   AMP PEAK 16(17P11.2) MUTATED AMP PEAK 16(17P11.2) WILD-TYPE
  R0                           31                            282
  R1                            0                              3
  R2                            2                             22
  RX                            1                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(17P11.2) MUTATED                                  1     1
  AMP PEAK 16(17P11.2) WILD-TYPE                                0    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(17P11.2) MUTATED                           6    22
  AMP PEAK 16(17P11.2) WILD-TYPE                        44   189
D16V12, multiclass
                                  clus
vv                                 AMP PEAK 16(17P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      22
                                  clus
vv                                 AMP PEAK 16(17P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       189
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = AMP PEAK 17(17Q12) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(17Q12) MUTATED    90  15
  AMP PEAK 17(17Q12) WILD-TYPE 245  72
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                         105                          317 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                          15                           72 
$`AMP PEAK 17(17Q12) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2686 
        5.06         5.26        43.76        43.43        17.79        16.04 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 
       36.53        14.53        30.44        29.19        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3494 
       27.09        25.08        25.18        24.69        20.28         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3517 TCGA-AA-3524 TCGA-AA-3532 
       37.05         1.02        58.03        38.99        36.03        29.00 
TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 
       12.99        24.00        23.01        15.02        36.00        85.05 
TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3869 
       35.05         1.02        17.03         0.99        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 
       18.05        12.99        34.03         2.01        50.99        13.05 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01F TCGA-AA-A01G 
       27.02        27.02        17.03        21.99        32.02        12.00 
TCGA-AA-A01S TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 
        1.02         0.92        41.00         4.21         0.79         0.10 
TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 
        0.43        16.31         6.87        61.41        12.10        29.56 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4750 
        3.19         2.24         0.07         1.35       102.44         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       13.02        29.06        22.03        17.03        14.04        29.03 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5539 
       21.99        14.99        13.05        11.08        11.01        19.59 
TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       11.51        18.25         1.32        15.12         4.50        17.13 
TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A285 
       14.30        13.41        24.43        38.20       130.65         6.12 
TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
       95.18         1.55        74.56        61.87        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A6GB 
       39.42        35.93        36.00        26.43        46.75         5.59 
TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-RU-A8FL 
        5.19        17.29        30.28 

$`AMP PEAK 17(17Q12) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       37.02        46.65        23.38        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        15.52        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.45        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 
       22.06        22.52        24.13         8.38        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        34.03        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       33.99        21.01        13.02        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.05        47.01        11.01         5.98        37.05        19.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 
        5.03        26.99        19.04         0.99         0.99         0.99 
TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       25.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       14.93         0.99        33.07        36.03        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        17.03        29.98        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       21.99        16.08        34.06        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07         7.96        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y 
        2.96        39.98         2.01         5.03        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 
       18.05        40.96         0.07        21.37        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        1.58         1.02         0.76         0.20         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       14.50        27.09         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 
       65.00        62.79        49.41         6.77       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         3.06         2.14         3.25         3.29 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.26         0.33         0.10        17.56        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       26.04        27.02        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        10.06        12.03        14.99        12.26        13.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 
       20.19        20.42        17.75         7.92        17.85        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.04         9.44        11.64         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       10.26       119.70        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67         1.28         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
      107.67        28.21         8.35        82.39        23.51        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 
       53.62        44.68        51.75        36.72        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
        4.11        10.98        10.52         2.79         5.98         1.32 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        26.99         6.64        14.76        67.00 

  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                      130.65                       140.38 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                       19.59                        19.66 
[1] "0.1 - 130.7 (19.6)" "0.1 - 140.4 (19.7)"
[1] "hr=" "1.5"
D17V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 17(17Q12) MUTATED        14        0        4        29         1
  AMP PEAK 17(17Q12) WILD-TYPE      58        1       24       102         7
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(17Q12) MUTATED           1         4          4         16
  AMP PEAK 17(17Q12) WILD-TYPE         0        17          8         39
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 17(17Q12) MUTATED           11       17         6         1
  AMP PEAK 17(17Q12) WILD-TYPE         27       26        12         1
D17V3, multiclass
            clus
vv           AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  STAGE I                            14                           58
  STAGE IA                            0                            1
  STAGE II                            4                           24
  STAGE IIA                          29                          102
  STAGE IIB                           1                            7
  STAGE IIC                           1                            0
  STAGE III                           4                           17
  STAGE IIIA                          4                            8
  STAGE IIIB                         16                           39
  STAGE IIIC                         11                           27
  STAGE IV                           17                           26
  STAGE IVA                           6                           12
  STAGE IVB                           1                            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 17(17Q12) MUTATED     5  14  81  11
  AMP PEAK 17(17Q12) WILD-TYPE   6  62 219  40
D17V4, multiclass
    clus
vv   AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  T1                          5                            6
  T2                         14                           62
  T3                         81                          219
  T4                         11                           40
[1] 4 2
[1] 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
  AMP PEAK 17(17Q12) MUTATED    56  29  25
  AMP PEAK 17(17Q12) WILD-TYPE 200  74  54
D17V5, multiclass
    clus
vv   AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  N0                         56                          200
  N1                         29                           74
  N2                         25                           54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 17(17Q12) MUTATED    69  19   4   1  18
  AMP PEAK 17(17Q12) WILD-TYPE 251  33   4   1  32
D17V6, multiclass
     clus
vv    AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  M0                          69                          251
  M1                          19                           33
  M1A                          4                            4
  M1B                          1                            1
  MX                          18                           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"
D17V7, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED    47  64
  AMP PEAK 17(17Q12) WILD-TYPE 160 168
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED     47   64
  AMP PEAK 17(17Q12) WILD-TYPE  160  168
        clus
vv       AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  FEMALE                         47                          160
  MALE                           64                          168
[1] 2 2
[1] FALSE
D17V8, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED    99  11
  AMP PEAK 17(17Q12) WILD-TYPE 279  48
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED     99   11
  AMP PEAK 17(17Q12) WILD-TYPE  279   48
                               clus
vv                              AMP PEAK 17(17Q12) MUTATED
  COLON ADENOCARCINOMA                                  99
  COLON MUCINOUS ADENOCARCINOMA                         11
                               clus
vv                              AMP PEAK 17(17Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                   279
  COLON MUCINOUS ADENOCARCINOMA                           48
[1] 2 2
[1] FALSE
D17V9, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED     1 110
  AMP PEAK 17(17Q12) WILD-TYPE   2 326
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED      1  110
  AMP PEAK 17(17Q12) WILD-TYPE    2  326
     clus
vv    AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  NO                           1                            2
  YES                        110                          326
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 17(17Q12) MUTATED    75   1  10   4
  AMP PEAK 17(17Q12) WILD-TYPE 238   2  14  21
D17V10, multiclass
    clus
vv   AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  R0                         75                          238
  R1                          1                            2
  R2                         10                           14
  RX                          4                           21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(17Q12) MUTATED                                  1     3
  AMP PEAK 17(17Q12) WILD-TYPE                                0     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(17Q12) MUTATED                          15    52
  AMP PEAK 17(17Q12) WILD-TYPE                        35   159
D17V12, multiclass
                                  clus
vv                                 AMP PEAK 17(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                15
  WHITE                                                    52
                                  clus
vv                                 AMP PEAK 17(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  35
  WHITE                                                     159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(17Q24.1) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(17Q24.1) MUTATED    87  12
  AMP PEAK 18(17Q24.1) WILD-TYPE 248  75
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                            99                            323 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                            12                             75 
$`AMP PEAK 18(17Q24.1) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2686 
        5.06         5.26        43.43        17.79        42.28        16.04 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 
       36.53        14.53        30.44        29.19        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3494 
       27.09        25.08        25.18        24.69        20.28         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3679 
       37.05         1.02        58.03        24.00        23.01        15.02 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3848 
       36.00        85.05        35.05         1.02        17.03         0.99 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 
       36.03         0.99        24.03        12.99        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A004 
       21.99        50.99        13.05        34.06        27.02        13.94 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A02J 
       17.03        21.99        12.00         1.02        37.02         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK 
        0.92        41.00         4.21         0.79         0.10         0.43 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-6715 
       14.50        16.31        61.41        29.56         2.24         0.07 
TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 
      102.44         8.02        13.02        29.06        22.03        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-CM-6676 
       14.04        29.03        21.99        14.99        13.05        11.08 
TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 
       11.01        12.26        19.59        11.51         1.32        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A285 
        4.50        17.13        14.30        13.41       130.65         6.12 
TCGA-DM-A28M TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       95.18        74.56        61.87        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A6GB 
       35.93        36.00        26.43        91.79        46.75         5.59 
TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-RU-A8FL 
        5.19        17.29        30.28 

$`AMP PEAK 18(17Q24.1) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 
       37.02        46.65        43.76        23.38        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       45.60        13.94        15.52        37.05        37.25        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.45        32.91        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6650 
       22.06        22.52        24.13         8.38        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       21.76        24.39        23.87        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       13.02        17.95        29.95        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 
       11.01         5.98        37.05        19.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
       19.04         0.99         0.99         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3851 
       15.95        38.99        36.95        37.02        14.93        33.07 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3976 
       26.01        24.00         2.01        20.98        16.08        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       25.02        24.00        19.07         7.96        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02         0.99        32.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02R 
       39.06        51.98         2.96        39.98         2.01        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       39.98        18.05        40.96         0.07        21.37        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        0.72         1.58         1.02         0.76         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.92        27.09         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82         5.19         5.52         6.87        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        62.79        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
      100.01         5.23        11.74         3.19         1.94         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.25         3.29         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56        40.34        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02         8.02        26.04        27.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       15.02        15.02        12.00        16.04        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 
       15.02        14.04        11.01        12.95        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       12.03        14.99        13.51        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       18.25         7.92        17.85        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        12.43         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64         1.51        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        23.51 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6321 
       43.07        53.62        44.68        51.75        36.72        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
        4.11        10.98        10.52         2.79         5.98         1.32 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        26.99         6.64        14.76        67.00 

  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                        130.65                         140.38 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                         19.59                          19.66 
[1] "0.1 - 130.7 (19.6)" "0.1 - 140.4 (19.7)"
[1] "hr=" "1.9"
D18V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 18(17Q24.1) MUTATED        16        0        4        27         1
  AMP PEAK 18(17Q24.1) WILD-TYPE      56        1       24       104         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(17Q24.1) MUTATED           1         4          4         16
  AMP PEAK 18(17Q24.1) WILD-TYPE         0        17          8         39
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 18(17Q24.1) MUTATED            8       12         5         1
  AMP PEAK 18(17Q24.1) WILD-TYPE         30       31        13         1
D18V3, multiclass
            clus
vv           AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  STAGE I                              16                             56
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            27                            104
  STAGE IIB                             1                              7
  STAGE IIC                             1                              0
  STAGE III                             4                             17
  STAGE IIIA                            4                              8
  STAGE IIIB                           16                             39
  STAGE IIIC                            8                             30
  STAGE IV                             12                             31
  STAGE IVA                             5                             13
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 18(17Q24.1) MUTATED     4  17  74   7
  AMP PEAK 18(17Q24.1) WILD-TYPE   7  59 226  44
D18V4, multiclass
    clus
vv   AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  T1                            4                              7
  T2                           17                             59
  T3                           74                            226
  T4                            7                             44
[1] 4 2
[1] 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
  AMP PEAK 18(17Q24.1) MUTATED    57  28  16
  AMP PEAK 18(17Q24.1) WILD-TYPE 199  75  63
D18V5, multiclass
    clus
vv   AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  N0                           57                            199
  N1                           28                             75
  N2                           16                             63
[1] 3 2
[1] 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 M1A M1B  MX
  AMP PEAK 18(17Q24.1) MUTATED    67  13   4   1  17
  AMP PEAK 18(17Q24.1) WILD-TYPE 253  39   4   1  33
D18V6, multiclass
     clus
vv    AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  M0                            67                            253
  M1                            13                             39
  M1A                            4                              4
  M1B                            1                              1
  MX                            17                             33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED    51  51
  AMP PEAK 18(17Q24.1) WILD-TYPE 156 181
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED     51   51
  AMP PEAK 18(17Q24.1) WILD-TYPE  156  181
        clus
vv       AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  FEMALE                           51                            156
  MALE                             51                            181
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED    93   8
  AMP PEAK 18(17Q24.1) WILD-TYPE 285  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED     93    8
  AMP PEAK 18(17Q24.1) WILD-TYPE  285   51
                               clus
vv                              AMP PEAK 18(17Q24.1) MUTATED
  COLON ADENOCARCINOMA                                    93
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              AMP PEAK 18(17Q24.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     285
  COLON MUCINOUS ADENOCARCINOMA                             51
[1] 2 2
[1] FALSE
D18V9, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED     1 101
  AMP PEAK 18(17Q24.1) WILD-TYPE   2 335
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED      1  101
  AMP PEAK 18(17Q24.1) WILD-TYPE    2  335
     clus
vv    AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  NO                             1                              2
  YES                          101                            335
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(17Q24.1) MUTATED    73   1   8   3
  AMP PEAK 18(17Q24.1) WILD-TYPE 240   2  16  22
D18V10, multiclass
    clus
vv   AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  R0                           73                            240
  R1                            1                              2
  R2                            8                             16
  RX                            3                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(17Q24.1) MUTATED                                  0     2
  AMP PEAK 18(17Q24.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(17Q24.1) MUTATED                          13    51
  AMP PEAK 18(17Q24.1) WILD-TYPE                        37   160
D18V12, multiclass
                                  clus
vv                                 AMP PEAK 18(17Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      51
                                  clus
vv                                 AMP PEAK 18(17Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       160
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = AMP PEAK 19(19P13.2) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(19P13.2) MUTATED    56  13
  AMP PEAK 19(19P13.2) WILD-TYPE 279  74
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            69                            353 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                            13                             74 
$`AMP PEAK 19(19P13.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 
        5.06         5.26        37.02        43.43        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6648 
       15.52        36.53        14.53        31.63        29.16        25.18 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3519 TCGA-AA-3662 TCGA-AA-3666 
       21.76        23.87        52.44         9.07         6.05         2.01 
TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3858 TCGA-AA-3972 TCGA-AA-3973 
       37.05        35.05         0.99        31.07        50.99        13.05 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A029 TCGA-AA-A02O 
       27.02        13.94        42.02        32.02        51.98         0.92 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-A8YK 
        1.58         1.02         0.43         0.46        16.31         6.87 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 
       61.41        29.56        11.74         3.06         1.35        40.34 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 
       21.99         2.01         8.02        13.02        29.06        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
        5.03        15.02        15.02        14.04        29.03        21.99 
TCGA-CM-6169 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6932 
       13.02        11.08        19.59        13.51        15.12        11.38 
TCGA-DM-A1D6 TCGA-DM-A28F TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 
       49.91        35.97        74.56        45.11        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A8F7 
       26.43        47.15         5.19 

$`AMP PEAK 19(19P13.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       46.65        43.76        23.38        17.79        42.28        35.11 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 
       13.94        37.05        37.25        16.04        34.65        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        24.16        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU 
       19.66        20.28        16.24        24.92        61.84         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04         0.99         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        53.00        17.03        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       21.99        16.08        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        19.07         7.96        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06         2.96        39.98         2.01         5.03 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 
       21.37         4.21        56.55         0.79         0.72         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.76         0.20         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13        83.80        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56       102.44        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       48.20        51.32        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 
       20.02        37.02        26.04         8.02        27.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 
       22.98        30.08        15.02        15.02        17.03        12.00 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       14.99        12.26        11.51        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        13.38        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       16.24        33.67         1.28         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6302 
      107.67        28.21         8.35        82.39        23.51        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       61.87        53.62        44.68        55.04        51.75        35.93 
TCGA-G4-6315 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.72        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       91.79        46.75        52.80         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         5.59         1.32         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       17.29         6.64        14.76        30.28        67.00 

  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                          0.43                           0.07 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                         74.56                         140.38 
  AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE 
                         19.59                          19.66 
[1] "0.4 - 74.6 (19.6)"  "0.1 - 140.4 (19.7)"
[1] "hr=" "1"  
D19V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 19(19P13.2) MUTATED         9        0        4        20         1
  AMP PEAK 19(19P13.2) WILD-TYPE      63        1       24       111         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(19P13.2) MUTATED           0         5          3         13
  AMP PEAK 19(19P13.2) WILD-TYPE         1        16          9         42
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 19(19P13.2) MUTATED            4        7         5         0
  AMP PEAK 19(19P13.2) WILD-TYPE         34       36        13         2
D19V3, multiclass
            clus
vv           AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  STAGE I                               9                             63
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            20                            111
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             5                             16
  STAGE IIIA                            3                              9
  STAGE IIIB                           13                             42
  STAGE IIIC                            4                             34
  STAGE IV                              7                             36
  STAGE IVA                             5                             13
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 19(19P13.2) MUTATED     2   9  54   8
  AMP PEAK 19(19P13.2) WILD-TYPE   9  67 246  43
D19V4, multiclass
    clus
vv   AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  T1                            2                              9
  T2                            9                             67
  T3                           54                            246
  T4                            8                             43
[1] 4 2
[1] 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
  AMP PEAK 19(19P13.2) MUTATED    37  26  10
  AMP PEAK 19(19P13.2) WILD-TYPE 219  77  69
D19V5, multiclass
    clus
vv   AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  N0                           37                            219
  N1                           26                             77
  N2                           10                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 19(19P13.2) MUTATED    45   9   3   0  15
  AMP PEAK 19(19P13.2) WILD-TYPE 275  43   5   2  35
D19V6, multiclass
     clus
vv    AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  M0                            45                            275
  M1                             9                             43
  M1A                            3                              5
  M1B                            0                              2
  MX                            15                             35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED    27  46
  AMP PEAK 19(19P13.2) WILD-TYPE 180 186
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED     27   46
  AMP PEAK 19(19P13.2) WILD-TYPE  180  186
        clus
vv       AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  FEMALE                           27                            180
  MALE                             46                            186
[1] 2 2
[1] FALSE
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED    66   7
  AMP PEAK 19(19P13.2) WILD-TYPE 312  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED     66    7
  AMP PEAK 19(19P13.2) WILD-TYPE  312   52
                               clus
vv                              AMP PEAK 19(19P13.2) MUTATED
  COLON ADENOCARCINOMA                                    66
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              AMP PEAK 19(19P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     312
  COLON MUCINOUS ADENOCARCINOMA                             52
[1] 2 2
[1] FALSE
D19V9, binary
                                cls
clus                               0   1
  AMP PEAK 19(19P13.2) MUTATED     1  72
  AMP PEAK 19(19P13.2) WILD-TYPE   2 364
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(19P13.2) MUTATED      1   72
  AMP PEAK 19(19P13.2) WILD-TYPE    2  364
     clus
vv    AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  NO                             1                              2
  YES                           72                            364
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(19P13.2) MUTATED    51   2   3   6
  AMP PEAK 19(19P13.2) WILD-TYPE 262   1  21  19
D19V10, multiclass
    clus
vv   AMP PEAK 19(19P13.2) MUTATED AMP PEAK 19(19P13.2) WILD-TYPE
  R0                           51                            262
  R1                            2                              1
  R2                            3                             21
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(19P13.2) MUTATED                                  0     2
  AMP PEAK 19(19P13.2) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(19P13.2) MUTATED                          11    42
  AMP PEAK 19(19P13.2) WILD-TYPE                        39   169
D19V12, multiclass
                                  clus
vv                                 AMP PEAK 19(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      42
                                  clus
vv                                 AMP PEAK 19(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(19Q13.11) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(19Q13.11) MUTATED    72  15
  AMP PEAK 20(19Q13.11) WILD-TYPE 263  72
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                             87                             335 
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                             15                              72 
$`AMP PEAK 20(19Q13.11) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 TCGA-A6-2683 
        5.06         5.26        37.02        43.43        45.60        15.52 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 
       16.04        34.65        36.53        14.53        31.63        29.16 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B 
       25.08        25.18        21.76        23.87        61.84        52.44 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3522 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3685 
       35.01        58.03        37.05        12.99        13.02        37.05 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3939 
       35.05         0.99        37.02        33.07        36.03        12.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z 
       50.99        13.05        18.05        27.02        42.02        21.99 
TCGA-AA-A01G TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O TCGA-AD-6888 TCGA-AD-6899 
       12.00        51.98        39.98         0.92         4.21         1.58 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK 
        1.02         0.43        14.50         0.20         5.52         6.87 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 
       61.41        29.56        11.74         3.06         1.35        40.34 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 
       21.99         2.01        37.02         8.02        13.02        29.06 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       16.01         5.03        15.02        15.02        14.04        29.03 
TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6928 
       21.99        11.08        19.59        15.12         4.50        11.64 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A28F TCGA-F4-6459 
       13.41        12.00        11.38       119.70        35.97         8.61 
TCGA-F4-6463 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 
       13.64        35.41        82.39        74.56        45.11        39.42 
TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A8F7 
       26.43        47.15         5.19 

$`AMP PEAK 20(19Q13.11) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        23.38        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 
       35.11        13.94        37.05        37.25        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6649 
       32.71        27.09        22.52        24.13         8.38        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05         1.02        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       13.02        38.99         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01         0.99        14.01        33.99        21.01        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01         5.98        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3819 
       85.05        26.99        19.04         0.99         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        36.95        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03         0.99        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
        2.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        17.03         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02         0.99        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E 
       33.04        35.01        26.01        37.02        39.06         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03        22.03        41.00        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.10         0.76         0.20         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       16.31         0.95        15.75        21.44        17.82         5.19 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        5.13        83.80        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56       102.44        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       48.20        51.32        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5344 TCGA-CM-5348 
       20.02        26.04         8.02        27.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 
       30.08        15.02        15.02        17.03        12.00        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       14.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        13.05        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       14.99        12.26        13.51        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25         1.32         7.92        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-7000 
       12.43        14.30         9.04         9.44         1.51        10.26 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 
      119.93        60.79       117.07        98.24        95.18        13.38 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       29.59        16.24        33.67         1.28         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21         8.35        23.51        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 
       53.62        44.68        55.04        51.75        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.00        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       91.79        46.75        52.80         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         5.59         1.32         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       17.29         6.64        14.76        30.28        67.00 

  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                           0.20                            0.07 
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                         119.70                          140.38 
  AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE 
                          21.76                           19.43 
[1] "0.2 - 119.7 (21.8)" "0.1 - 140.4 (19.4)"
[1] "hr=" "1.2"
D20V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 20(19Q13.11) MUTATED        12        0        4        29         0
  AMP PEAK 20(19Q13.11) WILD-TYPE      60        1       24       102         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(19Q13.11) MUTATED           0         3          4         14
  AMP PEAK 20(19Q13.11) WILD-TYPE         1        18          8         41
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 20(19Q13.11) MUTATED            8       11         5         0
  AMP PEAK 20(19Q13.11) WILD-TYPE         30       32        13         2
D20V3, multiclass
            clus
vv           AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  STAGE I                               12                              60
  STAGE IA                               0                               1
  STAGE II                               4                              24
  STAGE IIA                             29                             102
  STAGE IIB                              0                               8
  STAGE IIC                              0                               1
  STAGE III                              3                              18
  STAGE IIIA                             4                               8
  STAGE IIIB                            14                              41
  STAGE IIIC                             8                              30
  STAGE IV                              11                              32
  STAGE IVA                              5                              13
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 20(19Q13.11) MUTATED     2  14  68   8
  AMP PEAK 20(19Q13.11) WILD-TYPE   9  62 232  43
D20V4, multiclass
    clus
vv   AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  T1                             2                               9
  T2                            14                              62
  T3                            68                             232
  T4                             8                              43
[1] 4 2
[1] 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
  AMP PEAK 20(19Q13.11) MUTATED    48  29  14
  AMP PEAK 20(19Q13.11) WILD-TYPE 208  74  65
D20V5, multiclass
    clus
vv   AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  N0                            48                             208
  N1                            29                              74
  N2                            14                              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"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 20(19Q13.11) MUTATED    60  12   4   0  15
  AMP PEAK 20(19Q13.11) WILD-TYPE 260  40   4   2  35
D20V6, multiclass
     clus
vv    AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  M0                             60                             260
  M1                             12                              40
  M1A                             4                               4
  M1B                             0                               2
  MX                             15                              35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                 cls
clus                                0   1
  AMP PEAK 20(19Q13.11) MUTATED    36  56
  AMP PEAK 20(19Q13.11) WILD-TYPE 171 176
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.11) MUTATED     36   56
  AMP PEAK 20(19Q13.11) WILD-TYPE  171  176
        clus
vv       AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  FEMALE                            36                             171
  MALE                              56                             176
[1] 2 2
[1] FALSE
D20V8, binary
                                 cls
clus                                0   1
  AMP PEAK 20(19Q13.11) MUTATED    82  10
  AMP PEAK 20(19Q13.11) WILD-TYPE 296  49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.11) MUTATED     82   10
  AMP PEAK 20(19Q13.11) WILD-TYPE  296   49
                               clus
vv                              AMP PEAK 20(19Q13.11) MUTATED
  COLON ADENOCARCINOMA                                     82
  COLON MUCINOUS ADENOCARCINOMA                            10
                               clus
vv                              AMP PEAK 20(19Q13.11) WILD-TYPE
  COLON ADENOCARCINOMA                                      296
  COLON MUCINOUS ADENOCARCINOMA                              49
[1] 2 2
[1] FALSE
D20V9, binary
                                 cls
clus                                0   1
  AMP PEAK 20(19Q13.11) MUTATED     1  91
  AMP PEAK 20(19Q13.11) WILD-TYPE   2 345
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(19Q13.11) MUTATED      1   91
  AMP PEAK 20(19Q13.11) WILD-TYPE    2  345
     clus
vv    AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  NO                              1                               2
  YES                            91                             345
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(19Q13.11) MUTATED    68   1   4   6
  AMP PEAK 20(19Q13.11) WILD-TYPE 245   2  20  19
D20V10, multiclass
    clus
vv   AMP PEAK 20(19Q13.11) MUTATED AMP PEAK 20(19Q13.11) WILD-TYPE
  R0                            68                             245
  R1                             1                               2
  R2                             4                              20
  RX                             6                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(19Q13.11) MUTATED                                  0     2
  AMP PEAK 20(19Q13.11) WILD-TYPE                                1     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(19Q13.11) MUTATED                          12    52
  AMP PEAK 20(19Q13.11) WILD-TYPE                        38   159
D20V12, multiclass
                                  clus
vv                                 AMP PEAK 20(19Q13.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   12
  WHITE                                                       52
                                  clus
vv                                 AMP PEAK 20(19Q13.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     38
  WHITE                                                        159
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(20P12.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 21(20P12.1) MUTATED   150  45
  AMP PEAK 21(20P12.1) WILD-TYPE 185  42
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                           195                            227 
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                            45                             42 
$`AMP PEAK 21(20P12.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 
        5.06        37.02        43.76        43.43        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       45.60        13.94        15.52        16.04        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 
       32.45        30.44        27.09        25.08        24.16        24.69 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       20.28        61.84         9.63         5.03         1.02         1.02 
TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 
       58.03         6.97         1.02        19.07        29.00        29.00 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 
       14.01        21.01        13.02        23.01        20.98        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 
        6.05         2.01        14.01        50.04        47.05        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3818 
       37.05        19.00        36.00         5.03         0.99         0.99 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       38.99        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 
        0.99        31.07        17.03        27.02        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        26.01        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00U 
        7.96        13.94        18.05        17.03         4.01        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       14.99        21.99        15.02         0.99        12.00        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       33.04        26.01        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 
        0.92        41.00        39.98         0.07        21.37         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
        0.72         1.58         1.02         0.10         0.43        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4323 
       16.31         0.95         5.19         5.52         6.87         1.41 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 
        5.13        83.80        65.00        62.79        49.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
       29.56         3.19         2.24         3.06         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5912 
        0.07         0.26         1.35        17.56        40.34        48.20 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       20.02         8.02         8.02        13.02        29.06        22.98 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 
       16.04        21.99        14.04        11.01        11.08        11.01 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6536 
       14.99        12.26        19.59        20.19        17.75        17.85 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       12.49         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D8 
       11.64        13.41        10.26       119.70        24.43        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F 
        7.50        44.32       139.17         6.12        14.04        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 
      117.07        95.18         8.61        13.38        13.45         6.18 
TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6307 
        1.55        35.41       107.67        28.21        82.39        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 
       45.11        39.42        35.93        36.00        26.04        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC 
       91.79        46.75        47.15         4.11         5.59         1.32 
TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.19        26.99        17.29 

$`AMP PEAK 21(20P12.1) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2684 
        5.26        46.65        23.38        17.79        42.28        37.05 
TCGA-A6-2685 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       37.25        14.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        29.16        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       24.13         8.38        25.18        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       23.87        20.12        19.66        16.24        24.92        52.44 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 
        3.02        37.05         1.02        35.01        63.98        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
        8.05        19.07        34.03        26.01        12.99         0.99 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 
       33.99        24.00        17.95        29.95        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 
       61.02        78.08         6.97        54.02         0.92        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       11.01         5.98        85.05        26.99        19.04         0.99 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
       35.05        25.02         1.02        17.98        15.95        36.95 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 
       36.03        32.05        31.07        53.00        24.03        29.98 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       20.98        25.02        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 
       34.03        18.05        27.02        42.02         0.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       15.02        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02R 
        1.02        35.01        37.02        39.06        39.98        22.03 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6964 TCGA-AD-6965 
       18.05        40.96         4.21        56.55         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.46         0.92        27.09        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       17.82        75.25        50.37        58.39         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       22.36        61.41         6.77       100.01         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 
        1.94         3.25         0.33         0.10       102.44        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 
      124.27        23.05        37.02        26.04        27.02        22.03 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6167 
       30.08        16.01        15.02        12.00        29.03        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        15.02        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       10.06        12.03        13.51        11.51        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
        1.32         7.92        15.12         4.50        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       15.58        14.30         9.44         1.51        12.00        11.38 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65         7.76        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 
       60.79        98.24        11.11        13.64        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       29.59        16.24        33.67         1.28         0.53        19.43 
TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 
       44.68        51.75        36.72        26.43        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        52.80        10.98        10.52         2.79         5.98 
TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
        5.49         6.64        14.76        30.28        67.00 

  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                        139.17                         140.38 
  AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE 
                         16.08                          22.52 
[1] "0.1 - 139.2 (16.1)" "0.1 - 140.4 (22.5)"
[1] "hr=" "1.5"
D21V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 21(20P12.1) MUTATED        37        1       10        53         3
  AMP PEAK 21(20P12.1) WILD-TYPE      35        0       18        78         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(20P12.1) MUTATED           0         8         10         17
  AMP PEAK 21(20P12.1) WILD-TYPE         1        13          2         38
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 21(20P12.1) MUTATED           16       31        10         1
  AMP PEAK 21(20P12.1) WILD-TYPE         22       12         8         1
D21V3, multiclass
            clus
vv           AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  STAGE I                              37                             35
  STAGE IA                              1                              0
  STAGE II                             10                             18
  STAGE IIA                            53                             78
  STAGE IIB                             3                              5
  STAGE IIC                             0                              1
  STAGE III                             8                             13
  STAGE IIIA                           10                              2
  STAGE IIIB                           17                             38
  STAGE IIIC                           16                             22
  STAGE IV                             31                             12
  STAGE IVA                            10                              8
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 21(20P12.1) MUTATED     6  39 135  22
  AMP PEAK 21(20P12.1) WILD-TYPE   5  37 165  29
D21V4, multiclass
    clus
vv   AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  T1                            6                              5
  T2                           39                             37
  T3                          135                            165
  T4                           22                             29
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 21(20P12.1) MUTATED   112  53  38
  AMP PEAK 21(20P12.1) WILD-TYPE 144  50  41
D21V5, multiclass
    clus
vv   AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  N0                          112                            144
  N1                           53                             50
  N2                           38                             41
[1] 3 2
[1] 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 M1A M1B  MX
  AMP PEAK 21(20P12.1) MUTATED   134  34   6   1  25
  AMP PEAK 21(20P12.1) WILD-TYPE 186  18   2   1  25
D21V6, multiclass
     clus
vv    AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  M0                           134                            186
  M1                            34                             18
  M1A                            6                              2
  M1B                            1                              1
  MX                            25                             25
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                cls
clus                               0   1
  AMP PEAK 21(20P12.1) MUTATED    89 114
  AMP PEAK 21(20P12.1) WILD-TYPE 118 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20P12.1) MUTATED     89  114
  AMP PEAK 21(20P12.1) WILD-TYPE  118  118
        clus
vv       AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  FEMALE                           89                            118
  MALE                            114                            118
[1] 2 2
[1] FALSE
D21V8, binary
                                cls
clus                               0   1
  AMP PEAK 21(20P12.1) MUTATED   182  19
  AMP PEAK 21(20P12.1) WILD-TYPE 196  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20P12.1) MUTATED    182   19
  AMP PEAK 21(20P12.1) WILD-TYPE  196   40
                               clus
vv                              AMP PEAK 21(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                   182
  COLON MUCINOUS ADENOCARCINOMA                           19
                               clus
vv                              AMP PEAK 21(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     196
  COLON MUCINOUS ADENOCARCINOMA                             40
[1] 2 2
[1] FALSE
D21V9, binary
                                cls
clus                               0   1
  AMP PEAK 21(20P12.1) MUTATED     3 200
  AMP PEAK 21(20P12.1) WILD-TYPE   0 236
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 21(20P12.1) MUTATED      3  200
  AMP PEAK 21(20P12.1) WILD-TYPE    0  236
     clus
vv    AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  NO                             3                              0
  YES                          200                            236
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 21(20P12.1) MUTATED   140   2  18  11
  AMP PEAK 21(20P12.1) WILD-TYPE 173   1   6  14
D21V10, multiclass
    clus
vv   AMP PEAK 21(20P12.1) MUTATED AMP PEAK 21(20P12.1) WILD-TYPE
  R0                          140                            173
  R1                            2                              1
  R2                           18                              6
  RX                           11                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(20P12.1) MUTATED                                  1     7
  AMP PEAK 21(20P12.1) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(20P12.1) MUTATED                          20    96
  AMP PEAK 21(20P12.1) WILD-TYPE                        30   115
D21V12, multiclass
                                  clus
vv                                 AMP PEAK 21(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  20
  WHITE                                                      96
                                  clus
vv                                 AMP PEAK 21(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    30
  WHITE                                                       115
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(20P11.21) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 22(20P11.21) MUTATED   183  51
  AMP PEAK 22(20P11.21) WILD-TYPE 152  36
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                            234                             188 
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                             51                              36 
$`AMP PEAK 22(20P11.21) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 
       35.11        45.60        13.94        15.52        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.45        32.91        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        22.52        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       24.16        24.69        20.28        61.84         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 
        1.02         1.02         1.02        58.03         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 
       38.99        19.07        29.00        29.00        12.99        14.01 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 
       21.01        13.02        23.01        20.98        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 
        6.05         2.01        14.01        50.04        47.05        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05         0.99 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        0.99        25.02        38.99        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
        0.99        33.07         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       18.05        12.99        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K 
       24.00        27.02        19.07         7.96        13.94        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       17.03         4.01        17.03        14.99        21.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A01X 
       15.02         0.99        12.00        31.00        33.04        26.01 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6890 
       41.00        39.98        40.96         0.07        21.37         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.72         1.58         1.02         0.10         0.20         0.43 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D 
       14.50        16.31         0.95         0.20         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
        6.87         1.41         5.13        83.80        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       49.41        12.10        29.56         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.06         2.14         3.29         0.07         0.26         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 
       17.56        40.34        48.20        21.99        20.02         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
        8.02        13.02        29.06        22.03        22.98        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       29.03        16.04        21.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.01        11.08        11.01        10.06        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        11.51        20.19        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 
        7.92        12.49         7.53        12.39        10.13         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 
       11.64        13.41        10.26       119.70        24.43       130.65 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
       12.59         7.50       131.51       139.17         6.12        14.04 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
      119.93        35.97       117.07        95.18         8.61        13.38 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 
       13.45         6.18         1.55        33.67         1.28        35.41 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
      107.67        28.21         8.35        82.39        23.51        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.04        13.78        91.79        46.75        47.15         4.11 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         1.32         5.19        26.99        17.29         6.64 

$`AMP PEAK 22(20P11.21) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 
        5.26        46.65        23.38        42.28        37.05        37.25 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
        8.38        20.61        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3495 
       19.66        16.24        24.92        52.44         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       35.01        63.98        13.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3538 
       37.05        36.03         8.05        19.07        34.03        26.01 
TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 
        0.99        33.99        24.00        17.95        29.95        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 
       13.94        61.02         6.97        54.02         0.92        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       11.01         5.98        26.99        19.04         0.99        35.05 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3854 TCGA-AA-3855 
        1.02        17.98        15.95        36.95        36.03        32.05 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        24.03        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 
       33.01        26.01        24.00         2.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O 
       38.04        19.00        30.02        34.03        18.05        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P 
       42.02         0.99        34.98        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5820 
       22.03        18.05         4.21        56.55         0.76         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 
        0.92        27.09        15.75        21.44        17.82        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 
       50.37        58.39         5.65        32.94        22.36        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 
        6.77       100.01         5.23        11.74         3.25         0.33 
TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
        0.10       102.44        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
        2.93         2.01       124.27        23.05        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 
       27.02        30.08        15.02        12.00        14.99        12.99 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6530 
       12.95        13.05        11.08        12.03        13.51        20.42 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.50        17.13        16.14        15.58 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.44         1.51        12.00        11.38 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB 
       38.20        92.75        49.91        13.32       140.38        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K 
      135.65         7.76        26.47        81.37        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       11.11        13.64        35.87        16.31        29.59        16.24 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
        0.53        19.43        74.56        43.07        53.62        51.75 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       36.00        26.43        22.09        35.80        26.17        52.80 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5Z2 
       10.98        10.52         2.79         5.98         5.49        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 
       30.28        67.00 

  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE 
                         17.030                          23.215 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (23.2)"
[1] "hr=" "1.3"
D22V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 22(20P11.21) MUTATED        41        1       14        65         3
  AMP PEAK 22(20P11.21) WILD-TYPE      31        0       14        66         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(20P11.21) MUTATED           0         9         11         25
  AMP PEAK 22(20P11.21) WILD-TYPE         1        12          1         30
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 22(20P11.21) MUTATED           20       35        12         1
  AMP PEAK 22(20P11.21) WILD-TYPE         18        8         6         1
D22V3, multiclass
            clus
vv           AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  STAGE I                               41                              31
  STAGE IA                               1                               0
  STAGE II                              14                              14
  STAGE IIA                             65                              66
  STAGE IIB                              3                               5
  STAGE IIC                              0                               1
  STAGE III                              9                              12
  STAGE IIIA                            11                               1
  STAGE IIIB                            25                              30
  STAGE IIIC                            20                              18
  STAGE IV                              35                               8
  STAGE IVA                             12                               6
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 22(20P11.21) MUTATED     7  45 165  26
  AMP PEAK 22(20P11.21) WILD-TYPE   4  31 135  25
D22V4, multiclass
    clus
vv   AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  T1                             7                               4
  T2                            45                              31
  T3                           165                             135
  T4                            26                              25
[1] 4 2
[1] 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
  AMP PEAK 22(20P11.21) MUTATED   135  65  44
  AMP PEAK 22(20P11.21) WILD-TYPE 121  38  35
D22V5, multiclass
    clus
vv   AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  N0                           135                             121
  N1                            65                              38
  N2                            44                              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                               M0  M1 M1A M1B  MX
  AMP PEAK 22(20P11.21) MUTATED   164  39   7   1  29
  AMP PEAK 22(20P11.21) WILD-TYPE 156  13   1   1  21
D22V6, multiclass
     clus
vv    AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  M0                            164                             156
  M1                             39                              13
  M1A                             7                               1
  M1B                             1                               1
  MX                             29                              21
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20P11.21) MUTATED   109 135
  AMP PEAK 22(20P11.21) WILD-TYPE  98  97
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20P11.21) MUTATED    109  135
  AMP PEAK 22(20P11.21) WILD-TYPE   98   97
        clus
vv       AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  FEMALE                           109                              98
  MALE                             135                              97
[1] 2 2
[1] FALSE
D22V8, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20P11.21) MUTATED   221  21
  AMP PEAK 22(20P11.21) WILD-TYPE 157  38
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20P11.21) MUTATED    221   21
  AMP PEAK 22(20P11.21) WILD-TYPE  157   38
                               clus
vv                              AMP PEAK 22(20P11.21) MUTATED
  COLON ADENOCARCINOMA                                    221
  COLON MUCINOUS ADENOCARCINOMA                            21
                               clus
vv                              AMP PEAK 22(20P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      157
  COLON MUCINOUS ADENOCARCINOMA                              38
[1] 2 2
[1] FALSE
D22V9, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20P11.21) MUTATED     3 241
  AMP PEAK 22(20P11.21) WILD-TYPE   0 195
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20P11.21) MUTATED      3  241
  AMP PEAK 22(20P11.21) WILD-TYPE    0  195
     clus
vv    AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  NO                              3                               0
  YES                           241                             195
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 22(20P11.21) MUTATED   167   2  20  12
  AMP PEAK 22(20P11.21) WILD-TYPE 146   1   4  13
D22V10, multiclass
    clus
vv   AMP PEAK 22(20P11.21) MUTATED AMP PEAK 22(20P11.21) WILD-TYPE
  R0                           167                             146
  R1                             2                               1
  R2                            20                               4
  RX                            12                              13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(20P11.21) MUTATED                                  1     7
  AMP PEAK 22(20P11.21) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(20P11.21) MUTATED                          24   121
  AMP PEAK 22(20P11.21) WILD-TYPE                        26    90
D22V12, multiclass
                                  clus
vv                                 AMP PEAK 22(20P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   24
  WHITE                                                      121
                                  clus
vv                                 AMP PEAK 22(20P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     26
  WHITE                                                         90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(20Q11.21) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(20Q11.21) MUTATED   241  61
  AMP PEAK 23(20Q11.21) WILD-TYPE  94  26
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                            302                             120 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                             61                              26 
$`AMP PEAK 23(20Q11.21) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 
        6.97         1.02        38.99         9.07        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
        0.99        35.05         0.99        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       18.05        12.99        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       24.00        27.02        19.07         7.96        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        21.99        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       32.02        12.00        31.00        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
        5.03         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        0.10         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
        0.95        15.75         0.20         5.19         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       75.25         1.41         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       62.79        49.41        12.10        29.56         5.23         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 
        0.26         1.35        17.56       102.44        40.34        48.20 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       21.99         2.01        20.02        37.02         8.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        5.03        15.02        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        17.75        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 
       17.85         4.50        17.13        12.49         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 
       10.13        12.43        14.30         9.04        11.64        13.41 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      131.51       139.17         6.12        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
       35.97       117.07        95.18         8.61        13.38        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45         6.18         1.55        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        1.28         0.53        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       82.39        23.51        61.87        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       39.42        35.93        36.72        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       13.78        91.79        46.75        47.15         4.11        10.52 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-RU-A8FL 
        6.64        30.28 

$`AMP PEAK 23(20Q11.21) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 
        5.26        46.65        23.38        42.28        37.05        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       33.53        22.09        22.06         8.38        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        16.24        24.92         3.02        35.01        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 
       13.02         1.02        24.03        37.05         8.05         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        61.02         6.97        54.02         0.92 
TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 
       11.01        26.99        19.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       15.95        36.03        53.00        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 
       33.01        26.01        24.00         2.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P 
       38.04        30.02        18.05         0.99        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F 
        1.02        35.01        35.01        39.06        22.03        18.05 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
       56.55         0.76         0.92        27.09        21.44        17.82 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 
       50.37        58.39         5.65        32.94        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 
      100.01        11.74         3.25         0.33         0.10        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14         2.93       124.27        23.05 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 
       26.04        27.02        15.02        12.00        12.95        13.05 
TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 
       12.03        20.42        16.14        15.58         9.44         1.51 
TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G 
       12.00       140.38       135.65         7.76        81.37        60.79 
TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6299 
       98.24        11.11        35.87        16.31        19.43        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       43.07        53.62        51.75        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 
       52.80        10.98         2.79         5.98        14.76        67.00 

  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                          18.05                           22.09 
[1] "0.1 - 139.2 (18.1)" "0.1 - 140.4 (22.1)"
[1] "hr=" "1.1"
D23V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 23(20Q11.21) MUTATED        51        1       16        84         3
  AMP PEAK 23(20Q11.21) WILD-TYPE      21        0       12        47         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(20Q11.21) MUTATED           1        14         12         39
  AMP PEAK 23(20Q11.21) WILD-TYPE         0         7          0         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 23(20Q11.21) MUTATED           30       38        16         1
  AMP PEAK 23(20Q11.21) WILD-TYPE          8        5         2         1
D23V3, multiclass
            clus
vv           AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  STAGE I                               51                              21
  STAGE IA                               1                               0
  STAGE II                              16                              12
  STAGE IIA                             84                              47
  STAGE IIB                              3                               5
  STAGE IIC                              1                               0
  STAGE III                             14                               7
  STAGE IIIA                            12                               0
  STAGE IIIB                            39                              16
  STAGE IIIC                            30                               8
  STAGE IV                              38                               5
  STAGE IVA                             16                               2
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 23(20Q11.21) MUTATED     7  57 217  31
  AMP PEAK 23(20Q11.21) WILD-TYPE   4  19  83  20
D23V4, multiclass
    clus
vv   AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  T1                             7                               4
  T2                            57                              19
  T3                           217                              83
  T4                            31                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 23(20Q11.21) MUTATED   168  83  61
  AMP PEAK 23(20Q11.21) WILD-TYPE  88  20  18
D23V5, multiclass
    clus
vv   AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  N0                           168                              88
  N1                            83                              20
  N2                            61                              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                               M0  M1 M1A M1B  MX
  AMP PEAK 23(20Q11.21) MUTATED   220  46   7   1  35
  AMP PEAK 23(20Q11.21) WILD-TYPE 100   6   1   1  15
D23V6, multiclass
     clus
vv    AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  M0                            220                             100
  M1                             46                               6
  M1A                             7                               1
  M1B                             1                               1
  MX                             35                              15
[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"
D23V7, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q11.21) MUTATED   142 171
  AMP PEAK 23(20Q11.21) WILD-TYPE  65  61
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q11.21) MUTATED    142  171
  AMP PEAK 23(20Q11.21) WILD-TYPE   65   61
        clus
vv       AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  FEMALE                           142                              65
  MALE                             171                              61
[1] 2 2
[1] FALSE
D23V8, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q11.21) MUTATED   286  25
  AMP PEAK 23(20Q11.21) WILD-TYPE  92  34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q11.21) MUTATED    286   25
  AMP PEAK 23(20Q11.21) WILD-TYPE   92   34
                               clus
vv                              AMP PEAK 23(20Q11.21) MUTATED
  COLON ADENOCARCINOMA                                    286
  COLON MUCINOUS ADENOCARCINOMA                            25
                               clus
vv                              AMP PEAK 23(20Q11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                       92
  COLON MUCINOUS ADENOCARCINOMA                              34
[1] 2 2
[1] FALSE
D23V9, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q11.21) MUTATED     3 310
  AMP PEAK 23(20Q11.21) WILD-TYPE   0 126
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q11.21) MUTATED      3  310
  AMP PEAK 23(20Q11.21) WILD-TYPE    0  126
     clus
vv    AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  NO                              3                               0
  YES                           310                             126
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 23(20Q11.21) MUTATED   221   2  21  14
  AMP PEAK 23(20Q11.21) WILD-TYPE  92   1   3  11
D23V10, multiclass
    clus
vv   AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE
  R0                           221                              92
  R1                             2                               1
  R2                            21                               3
  RX                            14                              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(20Q11.21) MUTATED                                  1     7
  AMP PEAK 23(20Q11.21) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(20Q11.21) MUTATED                          34   154
  AMP PEAK 23(20Q11.21) WILD-TYPE                        16    57
D23V12, multiclass
                                  clus
vv                                 AMP PEAK 23(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   34
  WHITE                                                      154
                                  clus
vv                                 AMP PEAK 23(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     16
  WHITE                                                         57
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = AMP PEAK 24(20Q12) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 24(20Q12) MUTATED   242  61
  AMP PEAK 24(20Q12) WILD-TYPE  93  26
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                         303                          119 
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                          61                           26 
$`AMP PEAK 24(20Q12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 
        6.97         1.02        38.99         9.07        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 
       37.05        19.00        36.00         5.03        85.05         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       35.05         0.99        25.02        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
       14.93        17.03         0.99        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       31.07        31.07        17.03        24.03        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       12.99        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       27.02        19.07         7.96        13.94        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
       18.05        17.03         4.01        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        21.99        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       31.00        31.00         1.02        33.04        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       41.00        39.98        40.96         0.07        21.37         4.21 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        0.79         0.72         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.43         0.46        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 
        0.20         5.19         5.52         6.87        75.25         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
       49.41        12.10        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         2.14         3.29         0.07         0.26 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 
        1.35        17.56       102.44        40.34        48.20        21.99 
TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
        2.01        20.02        37.02         8.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        16.01         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        11.08        11.08        11.01        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       14.99        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.50        17.13        12.49         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 
       12.43        14.30         9.04        11.64        13.41        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59         7.50        44.32       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      139.17         6.12        14.04        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
      117.07        95.18         8.61        13.38        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        1.28         0.53        35.41       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
       82.39        23.51        74.56        61.87        44.68        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       45.11        39.42        35.93        36.72        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.04        13.78        91.79        46.75        47.15         4.11 
TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
       10.52         5.59         1.32         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       17.29         6.64        30.28 

$`AMP PEAK 24(20Q12) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 
        5.26        46.65        23.38        42.28        37.05        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       33.53        22.09        22.06         8.38        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        16.24        24.92         3.02        35.01        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 
       13.02         1.02        24.03        37.05         8.05         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        61.02         6.97        54.02         0.92 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 
       11.01         5.98        26.99        19.04         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 
       17.98        15.95        36.03        53.00        29.98        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 
        2.01        33.01        26.01        24.00         2.01        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 
       27.02        38.04        30.02        18.05         0.99        34.98 
TCGA-AA-A01D TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 
        0.99        38.07         1.02        35.01        35.01        39.06 
TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
       22.03        18.05        56.55         0.76         0.92        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5407 
       21.44        17.82        50.37        58.39        32.94        61.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
        6.77       100.01        11.74         3.25         0.33         0.10 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 
       23.05        26.04        27.02        15.02        12.00        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 
       13.05        12.03        20.42        16.14        15.58         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C 
        1.51        12.00       140.38       135.65         7.76        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 
       60.79        98.24        11.11        35.87        19.43        43.07 
TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       53.62        51.75        22.09        35.80        26.17        52.80 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 
       10.98         2.79         5.98        14.76        67.00 

  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                        0.07                         0.10 
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                      139.17                       140.38 
  AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE 
                       18.05                        22.09 
[1] "0.1 - 139.2 (18.1)" "0.1 - 140.4 (22.1)"
[1] "hr=" "1"  
D24V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 24(20Q12) MUTATED        51        1       16        85         3
  AMP PEAK 24(20Q12) WILD-TYPE      21        0       12        46         5
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(20Q12) MUTATED           1        13         12         39
  AMP PEAK 24(20Q12) WILD-TYPE         0         8          0         16
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 24(20Q12) MUTATED           30       38        17         1
  AMP PEAK 24(20Q12) WILD-TYPE          8        5         1         1
D24V3, multiclass
            clus
vv           AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  STAGE I                            51                           21
  STAGE IA                            1                            0
  STAGE II                           16                           12
  STAGE IIA                          85                           46
  STAGE IIB                           3                            5
  STAGE IIC                           1                            0
  STAGE III                          13                            8
  STAGE IIIA                         12                            0
  STAGE IIIB                         39                           16
  STAGE IIIC                         30                            8
  STAGE IV                           38                            5
  STAGE IVA                          17                            1
  STAGE IVB                           1                            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 24(20Q12) MUTATED     7  57 217  32
  AMP PEAK 24(20Q12) WILD-TYPE   4  19  83  19
D24V4, multiclass
    clus
vv   AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  T1                          7                            4
  T2                         57                           19
  T3                        217                           83
  T4                         32                           19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 24(20Q12) MUTATED   169  83  61
  AMP PEAK 24(20Q12) WILD-TYPE  87  20  18
D24V5, multiclass
    clus
vv   AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  N0                        169                           87
  N1                         83                           20
  N2                         61                           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                            M0  M1 M1A M1B  MX
  AMP PEAK 24(20Q12) MUTATED   220  47   7   1  35
  AMP PEAK 24(20Q12) WILD-TYPE 100   5   1   1  15
D24V6, multiclass
     clus
vv    AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  M0                         220                          100
  M1                          47                            5
  M1A                          7                            1
  M1B                          1                            1
  MX                          35                           15
[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"
D24V7, binary
                              cls
clus                             0   1
  AMP PEAK 24(20Q12) MUTATED   142 172
  AMP PEAK 24(20Q12) WILD-TYPE  65  60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(20Q12) MUTATED    142  172
  AMP PEAK 24(20Q12) WILD-TYPE   65   60
        clus
vv       AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  FEMALE                        142                           65
  MALE                          172                           60
[1] 2 2
[1] FALSE
D24V8, binary
                              cls
clus                             0   1
  AMP PEAK 24(20Q12) MUTATED   288  24
  AMP PEAK 24(20Q12) WILD-TYPE  90  35
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(20Q12) MUTATED    288   24
  AMP PEAK 24(20Q12) WILD-TYPE   90   35
                               clus
vv                              AMP PEAK 24(20Q12) MUTATED
  COLON ADENOCARCINOMA                                 288
  COLON MUCINOUS ADENOCARCINOMA                         24
                               clus
vv                              AMP PEAK 24(20Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    90
  COLON MUCINOUS ADENOCARCINOMA                           35
[1] 2 2
[1] FALSE
D24V9, binary
                              cls
clus                             0   1
  AMP PEAK 24(20Q12) MUTATED     3 311
  AMP PEAK 24(20Q12) WILD-TYPE   0 125
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 24(20Q12) MUTATED      3  311
  AMP PEAK 24(20Q12) WILD-TYPE    0  125
     clus
vv    AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  NO                           3                            0
  YES                        311                          125
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 24(20Q12) MUTATED   222   2  21  14
  AMP PEAK 24(20Q12) WILD-TYPE  91   1   3  11
D24V10, multiclass
    clus
vv   AMP PEAK 24(20Q12) MUTATED AMP PEAK 24(20Q12) WILD-TYPE
  R0                        222                           91
  R1                          2                            1
  R2                         21                            3
  RX                         14                           11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(20Q12) MUTATED                                  1     7
  AMP PEAK 24(20Q12) WILD-TYPE                                0     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(20Q12) MUTATED                          34   157
  AMP PEAK 24(20Q12) WILD-TYPE                        16    54
D24V12, multiclass
                                  clus
vv                                 AMP PEAK 24(20Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                34
  WHITE                                                   157
                                  clus
vv                                 AMP PEAK 24(20Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = AMP PEAK 25(20Q13.12) MUTATION ANALYSIS
D25V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 25(20Q13.12) MUTATED   243  63
  AMP PEAK 25(20Q13.12) WILD-TYPE  92  24
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                            306                             116 
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                             63                              24 
$`AMP PEAK 25(20Q13.12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        37.02        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        15.52        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       34.65        36.53        14.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       29.19        23.61        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       24.13        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.69        23.87        20.28        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        5.03         1.02         1.02        37.05         1.02        58.03 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3524 TCGA-AA-3526 
        6.97         1.02        38.99         9.07        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       15.02        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
        0.99        35.05         0.99        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       18.05        12.99        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D 
       24.00        27.02        19.07         7.96        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       34.03        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        21.99        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       32.02        12.00        31.00        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        51.98         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
        5.03         0.92        41.00        39.98        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37         4.21         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        0.10         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
        0.95        15.75         0.20         5.19         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       75.25         1.41         5.65         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        3.29         0.07         0.26         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
       40.34        48.20        21.99         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02         8.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6676 
       12.99        13.02        15.02        14.04        11.01        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       13.51        11.51        20.19        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        7.92        15.12        17.85         4.50        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
        7.53        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.41        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
        7.50        44.32       131.51       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
       26.47       119.93        35.97       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
       13.38        13.64        13.45         6.18         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
      107.67        28.21         8.35        82.39        23.51        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       61.87        44.68        55.04        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 
       36.72        36.00        26.43        26.04        13.78        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        47.15         4.11        10.52         5.59         1.32 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
        5.19         5.49        26.99        17.29         6.64        30.28 

$`AMP PEAK 25(20Q13.12) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 
        5.26        46.65        23.38        42.28        37.05        31.63 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       33.53        22.09        22.06         8.38        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        16.24        24.92         3.02        35.01        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 
       13.02         1.02        24.03        37.05         8.05         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3680 
       17.95        29.95        61.02         6.97         0.92        11.01 
TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 
        5.98        26.99        19.04         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       15.95        36.03        53.00        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 
       33.01        26.01        24.00         2.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P 
       38.04        30.02        18.05         0.99        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F 
        1.02        35.01        35.01        39.06        22.03        18.05 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
       56.55         0.76         0.92        27.09        21.44        17.82 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       50.37        58.39        32.94        61.41         6.77       100.01 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        3.25         0.33         0.10        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 
       21.14         2.93       124.27        23.05        26.04        27.02 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 
       15.02        12.00        12.95        13.05        12.03        20.42 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 
       16.14        15.58         9.44         1.51        12.00       140.38 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 
      135.65         7.76        81.37        60.79        98.24        11.11 
TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 
       35.87        19.43        43.07        53.62        51.75        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA 
       35.80        26.17        52.80        10.98         2.79         5.98 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       14.76        67.00 

  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE 
                          18.05                           22.09 
[1] "0.1 - 139.2 (18.1)" "0.1 - 140.4 (22.1)"
[1] "hr=" "1.1"
D25V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 25(20Q13.12) MUTATED        51        1       17        85         3
  AMP PEAK 25(20Q13.12) WILD-TYPE      21        0       11        46         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(20Q13.12) MUTATED           1        13         12         39
  AMP PEAK 25(20Q13.12) WILD-TYPE         0         8          0         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 25(20Q13.12) MUTATED           31       39        17         1
  AMP PEAK 25(20Q13.12) WILD-TYPE          7        4         1         1
D25V3, multiclass
            clus
vv           AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  STAGE I                               51                              21
  STAGE IA                               1                               0
  STAGE II                              17                              11
  STAGE IIA                             85                              46
  STAGE IIB                              3                               5
  STAGE IIC                              1                               0
  STAGE III                             13                               8
  STAGE IIIA                            12                               0
  STAGE IIIB                            39                              16
  STAGE IIIC                            31                               7
  STAGE IV                              39                               4
  STAGE IVA                             17                               1
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 25(20Q13.12) MUTATED     7  57 219  33
  AMP PEAK 25(20Q13.12) WILD-TYPE   4  19  81  18
D25V4, multiclass
    clus
vv   AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  T1                             7                               4
  T2                            57                              19
  T3                           219                              81
  T4                            33                              18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 25(20Q13.12) MUTATED   170  83  63
  AMP PEAK 25(20Q13.12) WILD-TYPE  86  20  16
D25V5, multiclass
    clus
vv   AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  N0                           170                              86
  N1                            83                              20
  N2                            63                              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 25(20Q13.12) MUTATED   222  48   7   1  35
  AMP PEAK 25(20Q13.12) WILD-TYPE  98   4   1   1  15
D25V6, multiclass
     clus
vv    AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  M0                            222                              98
  M1                             48                               4
  M1A                             7                               1
  M1B                             1                               1
  MX                             35                              15
[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"
D25V7, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.12) MUTATED   144 173
  AMP PEAK 25(20Q13.12) WILD-TYPE  63  59
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.12) MUTATED    144  173
  AMP PEAK 25(20Q13.12) WILD-TYPE   63   59
        clus
vv       AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  FEMALE                           144                              63
  MALE                             173                              59
[1] 2 2
[1] FALSE
D25V8, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.12) MUTATED   290  25
  AMP PEAK 25(20Q13.12) WILD-TYPE  88  34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.12) MUTATED    290   25
  AMP PEAK 25(20Q13.12) WILD-TYPE   88   34
                               clus
vv                              AMP PEAK 25(20Q13.12) MUTATED
  COLON ADENOCARCINOMA                                    290
  COLON MUCINOUS ADENOCARCINOMA                            25
                               clus
vv                              AMP PEAK 25(20Q13.12) WILD-TYPE
  COLON ADENOCARCINOMA                                       88
  COLON MUCINOUS ADENOCARCINOMA                              34
[1] 2 2
[1] FALSE
D25V9, binary
                                 cls
clus                                0   1
  AMP PEAK 25(20Q13.12) MUTATED     3 314
  AMP PEAK 25(20Q13.12) WILD-TYPE   0 122
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 25(20Q13.12) MUTATED      3  314
  AMP PEAK 25(20Q13.12) WILD-TYPE    0  122
     clus
vv    AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  NO                              3                               0
  YES                           314                             122
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 25(20Q13.12) MUTATED   224   2  21  14
  AMP PEAK 25(20Q13.12) WILD-TYPE  89   1   3  11
D25V10, multiclass
    clus
vv   AMP PEAK 25(20Q13.12) MUTATED AMP PEAK 25(20Q13.12) WILD-TYPE
  R0                           224                              89
  R1                             2                               1
  R2                            21                               3
  RX                            14                              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(20Q13.12) MUTATED                                  1     7
  AMP PEAK 25(20Q13.12) WILD-TYPE                                0     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(20Q13.12) MUTATED                          34   158
  AMP PEAK 25(20Q13.12) WILD-TYPE                        16    53
D25V12, multiclass
                                  clus
vv                                 AMP PEAK 25(20Q13.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   34
  WHITE                                                      158
                                  clus
vv                                 AMP PEAK 25(20Q13.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                     16
  WHITE                                                         53
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   119  39
  DEL PEAK  1(1P36.11) WILD-TYPE 216  48
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           158                            264 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            39                             48 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       43.76        17.79        44.91        35.11        13.94        15.52 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       36.53        14.53        32.45        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 
       29.16        22.52        24.13        25.18        21.76        23.87 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3526 
       52.44         5.03        38.99         9.07        37.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       19.07        34.03        14.01        13.02        24.00        23.01 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       19.99         2.01        14.01        50.04        47.01        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3837 
       19.00        36.00        85.05         0.99        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
       36.95        37.02         0.99        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3930 
       31.07        31.07        17.03        24.03        29.98         2.01 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       12.99         2.01         2.01        21.99        50.99        13.05 
TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C 
       26.01         7.96        34.03        42.02        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       32.02        31.00        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 
        2.01         5.03        41.00        40.96         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        1.02         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 
        5.52         5.65         5.13        22.36        65.00        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23         3.19         2.24         3.06         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 
        3.29         0.07         0.26         1.35        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
        8.02         8.02        13.02        22.03        30.08         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       15.02        14.04        29.03        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       11.08        10.06        12.03        14.99        13.51        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6541 
       17.75         1.32         7.92        15.12        17.85        15.58 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 
       12.43        14.30        13.41        11.38        92.75        49.91 
TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28H TCGA-DM-A28M 
       44.32       139.17         6.12        26.47       117.07        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6855 
       13.38        11.11         1.55        29.59         1.28        35.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6315 
        8.35        82.39        23.51        61.87        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
       36.00        91.79        46.75         4.11        10.98         5.98 
TCGA-NH-A8F8 TCGA-QG-A5YV 
        5.49        26.99 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       42.28        45.60        37.05        37.25        16.04        34.65 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        30.44        33.53        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
       27.09         8.38        25.08        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84         9.63         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3532 
       13.02         1.02        24.03        36.03         8.05        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99         0.99        33.99        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       17.95        29.95        20.98        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.05         6.97        54.02         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       15.02        11.01         5.98         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       14.93        17.03        36.03        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       34.03        16.08        34.06        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        21.99        34.98         0.99        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        39.06        51.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       18.05         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.10         0.76         0.92        27.09         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
        0.20        21.44        17.82         5.19         6.87        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-5403 
       50.37        58.39         1.41        32.94        83.80        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 
       61.41        49.41         6.77       100.01        11.74         1.94 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.25         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        48.20        51.32        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        20.02        37.02        26.04        27.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       29.06        22.98        16.01        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 
       14.04        12.95        13.05        11.08        11.01        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 
       19.59        11.51        20.42        18.25         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 
       12.49        16.14         7.53        12.39        10.13         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C 
        7.50       131.51       135.65         7.76        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 
      119.93        35.97        60.79        98.24         8.61        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       13.45         6.18        35.87        16.31        16.24        33.67 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 
        0.53        19.43       107.67        28.21        74.56        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       47.15        52.80        10.52         2.79         5.59         1.32 
TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
        5.19        17.29         6.64        14.76        30.28        67.00 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        139.17                         140.38 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         17.77                          20.35 
[1] "0.1 - 139.2 (17.8)" "0.1 - 140.4 (20.4)"
[1] "hr=" "1.6"
D26V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  1(1P36.11) MUTATED        21        0        5        45         1
  DEL PEAK  1(1P36.11) WILD-TYPE      51        1       23        86         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED           1         8          4         18
  DEL PEAK  1(1P36.11) WILD-TYPE         0        13          8         37
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.11) MUTATED           17       29        10         0
  DEL PEAK  1(1P36.11) WILD-TYPE         21       14         8         2
D26V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              21                             51
  STAGE IA                              0                              1
  STAGE II                              5                             23
  STAGE IIA                            45                             86
  STAGE IIB                             1                              7
  STAGE IIC                             1                              0
  STAGE III                             8                             13
  STAGE IIIA                            4                              8
  STAGE IIIB                           18                             37
  STAGE IIIC                           17                             21
  STAGE IV                             29                             14
  STAGE IVA                            10                              8
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED     3  26 113  21
  DEL PEAK  1(1P36.11) WILD-TYPE   8  50 187  30
D26V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            3                              8
  T2                           26                             50
  T3                          113                            187
  T4                           21                             30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK  1(1P36.11) MUTATED    82  42  39
  DEL PEAK  1(1P36.11) WILD-TYPE 174  61  40
D26V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           82                            174
  N1                           42                             61
  N2                           39                             40
[1] 3 2
[1] 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 M1A M1B  MX
  DEL PEAK  1(1P36.11) MUTATED   105  35   4   0  18
  DEL PEAK  1(1P36.11) WILD-TYPE 215  17   4   2  32
D26V6, multiclass
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                           105                            215
  M1                            35                             17
  M1A                            4                              4
  M1B                            0                              2
  MX                            18                             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"
D26V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED    70  93
  DEL PEAK  1(1P36.11) WILD-TYPE 137 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     70   93
  DEL PEAK  1(1P36.11) WILD-TYPE  137  139
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           70                            137
  MALE                             93                            139
[1] 2 2
[1] FALSE
D26V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   151  11
  DEL PEAK  1(1P36.11) WILD-TYPE 227  48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    151   11
  DEL PEAK  1(1P36.11) WILD-TYPE  227   48
                               clus
vv                              DEL PEAK  1(1P36.11) MUTATED
  COLON ADENOCARCINOMA                                   151
  COLON MUCINOUS ADENOCARCINOMA                           11
                               clus
vv                              DEL PEAK  1(1P36.11) WILD-TYPE
  COLON ADENOCARCINOMA                                     227
  COLON MUCINOUS ADENOCARCINOMA                             48
[1] 2 2
[1] FALSE
D26V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     1 162
  DEL PEAK  1(1P36.11) WILD-TYPE   2 274
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      1  162
  DEL PEAK  1(1P36.11) WILD-TYPE    2  274
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             1                              2
  YES                          162                            274
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   108   1  14  11
  DEL PEAK  1(1P36.11) WILD-TYPE 205   2  10  14
D26V10, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          108                            205
  R1                            1                              2
  R2                           14                             10
  RX                           11                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.11) MUTATED                                  1     7
  DEL PEAK  1(1P36.11) WILD-TYPE                                0     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED                          15    79
  DEL PEAK  1(1P36.11) WILD-TYPE                        35   132
D26V12, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      79
                                  clus
vv                                 DEL PEAK  1(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       132
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = DEL PEAK  2(1P33) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1P33) MUTATED    83  31
  DEL PEAK  2(1P33) WILD-TYPE 252  56
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        114                         308 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         31                          56 
$`DEL PEAK  2(1P33) MUTATED`
TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       43.76        35.11        15.52        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6138 
       14.53        32.45        29.19        23.61        29.16        22.52 
TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 
       21.76        23.87         5.03        38.99         9.07        37.05 
TCGA-AA-3525 TCGA-AA-3549 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 
        8.05        21.01        19.99        50.04        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 
       85.05         0.99        38.99        36.95        37.02         0.99 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 
       33.07        32.05        31.07        17.03        24.03         2.01 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00F 
       12.99         2.01        21.99        13.05         7.96        34.03 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       42.02        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 
        2.96         2.01        22.03        41.00         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D 
        1.02         0.20         0.43        14.50        16.31         5.52 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
        5.65         5.13        62.79        12.10        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 
        3.19         2.24         3.06         2.14         0.26         2.01 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
        8.02        13.02        22.03         5.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       29.03        13.02        15.02        11.08        11.08        10.06 
TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6924 TCGA-D5-6929 
       13.51         1.32        15.12        17.85        14.30        13.41 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A288 TCGA-DM-A28A 
       11.38        38.20        92.75        49.91        14.04        26.47 
TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
       35.97        13.38         1.55        35.41         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       23.51        61.87        35.93        36.72        36.00        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV 
       46.75         4.11        10.98         5.98         5.49        26.99 

$`DEL PEAK  2(1P33) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 
       17.79        42.28        44.91        45.60        13.94        37.05 
TCGA-A6-3807 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       34.65        32.91        31.63        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.06        32.71        27.09        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
        1.02        24.03        36.03        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 
        1.02        17.98        15.95        14.93        17.03        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        53.00        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       31.00        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
       20.98        34.03        16.08        50.99        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02         0.99        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
       51.98        39.98         5.03         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       40.96         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
        0.10         0.76         0.46         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
       15.75         0.20        21.44        17.82         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 
       75.25        50.37        58.39         1.41        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        65.00        61.41        49.41         6.77       100.01 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       11.74         1.94         3.25         3.29         0.07         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02         8.02        26.04 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        29.06        22.98        30.08        16.01        15.02 
TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       11.01        12.03        14.99        12.26        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6537 
       20.19        20.42        17.75        18.25         7.92         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43         9.04         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D7 
       12.00        10.26       119.70        24.43       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       12.59       140.38         7.50        44.32       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        7.76       139.17         6.12        81.37       119.93        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67         1.28         0.53        19.43       107.67        28.21 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       74.56        43.07        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       45.11        39.42        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80        10.52         2.79 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.59         1.32         5.19        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 
       30.28        67.00 

  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                       0.20                        0.07 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                      92.75                      140.38 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                     16.175                      20.155 
[1] "0.2 - 92.8 (16.2)"  "0.1 - 140.4 (20.2)"
[1] "hr=" "1.8"
D27V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  2(1P33) MUTATED        12        0        5        34         0
  DEL PEAK  2(1P33) WILD-TYPE      60        1       23        97         8
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P33) MUTATED           0         6          3         15
  DEL PEAK  2(1P33) WILD-TYPE         1        15          9         40
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  2(1P33) MUTATED           14       22         4         0
  DEL PEAK  2(1P33) WILD-TYPE         24       21        14         2
D27V3, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                           12                          60
  STAGE IA                           0                           1
  STAGE II                           5                          23
  STAGE IIA                         34                          97
  STAGE IIB                          0                           8
  STAGE IIC                          0                           1
  STAGE III                          6                          15
  STAGE IIIA                         3                           9
  STAGE IIIB                        15                          40
  STAGE IIIC                        14                          24
  STAGE IV                          22                          21
  STAGE IVA                          4                          14
  STAGE IVB                          0                           2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  2(1P33) MUTATED     3  15  85  16
  DEL PEAK  2(1P33) WILD-TYPE   8  61 215  35
D27V4, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T1                         3                           8
  T2                        15                          61
  T3                        85                         215
  T4                        16                          35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK  2(1P33) MUTATED    57  32  30
  DEL PEAK  2(1P33) WILD-TYPE 199  71  49
D27V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        57                         199
  N1                        32                          71
  N2                        30                          49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK  2(1P33) MUTATED    76  24   2   0  17
  DEL PEAK  2(1P33) WILD-TYPE 244  28   6   2  33
D27V6, multiclass
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  M0                         76                         244
  M1                         24                          28
  M1A                         2                           6
  M1B                         0                           2
  MX                         17                          33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    53  66
  DEL PEAK  2(1P33) WILD-TYPE 154 166
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     53   66
  DEL PEAK  2(1P33) WILD-TYPE  154  166
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        53                         154
  MALE                          66                         166
[1] 2 2
[1] FALSE
D27V8, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   109  10
  DEL PEAK  2(1P33) WILD-TYPE 269  49
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    109   10
  DEL PEAK  2(1P33) WILD-TYPE  269   49
                               clus
vv                              DEL PEAK  2(1P33) MUTATED
  COLON ADENOCARCINOMA                                109
  COLON MUCINOUS ADENOCARCINOMA                        10
                               clus
vv                              DEL PEAK  2(1P33) WILD-TYPE
  COLON ADENOCARCINOMA                                  269
  COLON MUCINOUS ADENOCARCINOMA                          49
[1] 2 2
[1] FALSE
D27V9, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED     0 119
  DEL PEAK  2(1P33) WILD-TYPE   3 317
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED      0  119
  DEL PEAK  2(1P33) WILD-TYPE    3  317
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                          0                           3
  YES                       119                         317
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  2(1P33) MUTATED    77   1  10   7
  DEL PEAK  2(1P33) WILD-TYPE 236   2  14  18
D27V10, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                        77                         236
  R1                         1                           2
  R2                        10                          14
  RX                         7                          18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P33) MUTATED                                  1     4
  DEL PEAK  2(1P33) WILD-TYPE                                0     7
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P33) MUTATED                          15    57
  DEL PEAK  2(1P33) WILD-TYPE                        35   154
D27V12, multiclass
                                  clus
vv                                 DEL PEAK  2(1P33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               15
  WHITE                                                   57
                                  clus
vv                                 DEL PEAK  2(1P33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      7
  BLACK OR AFRICAN AMERICAN                                 35
  WHITE                                                    154
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = DEL PEAK  3(1P13.1) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1P13.1) MUTATED    84  26
  DEL PEAK  3(1P13.1) WILD-TYPE 251  61
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                          110                           312 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                           26                            61 
$`DEL PEAK  3(1P13.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-3810 
       37.02        43.76        35.11        15.52        37.25        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6651 
       14.53        32.45        29.19        23.61        22.52        21.76 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 
       23.87        52.44         5.03        38.99         9.07        37.05 
TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 
       21.01        13.94        19.99        50.04        37.05        19.00 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3860 
        0.99        38.99        37.02         0.99        32.05        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 
       17.03        24.03         2.01        12.99         2.01         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00Q TCGA-AA-A01C 
       21.99        13.05         7.96        38.04        42.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       32.02        31.00         1.02        33.04        26.01         2.96 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 
        2.01        41.00        40.96         0.79         1.02         0.20 
TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-A69D TCGA-AZ-4615 TCGA-AZ-4616 
        0.43         0.92        14.50         5.52        32.94         5.13 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       65.00        12.10        29.56         5.23         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 
        3.06         2.14         0.26         2.01         8.02        13.02 
TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       22.03        14.04        29.03        13.02        15.02        11.08 
TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 
       10.06        13.51        17.75         1.32        15.12        14.30 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A285 
       13.41        11.38        92.75        49.91       131.51         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6855 
       14.04        26.47        13.38         1.55        16.24        35.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 
        8.35        82.39        23.51        61.87        36.72        36.00 
TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA 
       26.04        91.79        46.75         4.11        10.98         5.98 
TCGA-NH-A8F8 TCGA-QG-A5YV 
        5.49        26.99 

$`DEL PEAK  3(1P13.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 
       42.28        44.91        45.60        13.94        37.05        16.04 
TCGA-A6-3807 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       34.65        32.91        31.63        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        20.61        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
        1.02        24.03        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       23.01        20.98        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
       85.05        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        36.95        14.93 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       17.03        33.07        36.03         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       27.02        29.98        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       26.01        24.00        20.98        34.03        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        13.94        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        17.03         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       14.99        21.99        34.98        15.02         0.99        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       31.00        38.07        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       39.06        51.98        39.98         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37         4.21        56.55 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-6004 
        0.72         1.58         0.10         0.76         0.46        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.65        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 
        6.77       100.01        11.74         1.94         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
        8.02        26.04        27.02        29.06        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       12.03        14.99        12.26        19.59        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.42        18.25         7.92        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38         7.50        44.32       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 
        6.18        35.87        16.31        29.59        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 
        0.53        19.43       107.67        28.21        74.56        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       35.93        26.43        22.09        13.78        35.80        26.17 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       47.15        52.80        10.52         2.79         5.59         1.32 
TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
        5.19        17.29         6.64        14.76        30.28        67.00 

  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE 
                       15.880                        20.155 
[1] "0.2 - 131.5 (15.9)" "0.1 - 140.4 (20.2)"
[1] "hr=" "1.4"
D28V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  3(1P13.1) MUTATED        12        0        5        31         0
  DEL PEAK  3(1P13.1) WILD-TYPE      60        1       23       100         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1P13.1) MUTATED           0         5          3         15
  DEL PEAK  3(1P13.1) WILD-TYPE         1        16          9         40
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  3(1P13.1) MUTATED           13       23         3         0
  DEL PEAK  3(1P13.1) WILD-TYPE         25       20        15         2
D28V3, multiclass
            clus
vv           DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  STAGE I                             12                            60
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           31                           100
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           3                             9
  STAGE IIIB                          15                            40
  STAGE IIIC                          13                            25
  STAGE IV                            23                            20
  STAGE IVA                            3                            15
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  3(1P13.1) MUTATED     3  15  82  14
  DEL PEAK  3(1P13.1) WILD-TYPE   8  61 218  37
D28V4, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  T1                           3                             8
  T2                          15                            61
  T3                          82                           218
  T4                          14                            37
[1] 4 2
[1] 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
  DEL PEAK  3(1P13.1) MUTATED    53  30  31
  DEL PEAK  3(1P13.1) WILD-TYPE 203  73  48
D28V5, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  N0                          53                           203
  N1                          30                            73
  N2                          31                            48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  3(1P13.1) MUTATED    73  25   1   0  15
  DEL PEAK  3(1P13.1) WILD-TYPE 247  27   7   2  35
D28V6, multiclass
     clus
vv    DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  M0                           73                           247
  M1                           25                            27
  M1A                           1                             7
  M1B                           0                             2
  MX                           15                            35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED    49  65
  DEL PEAK  3(1P13.1) WILD-TYPE 158 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED     49   65
  DEL PEAK  3(1P13.1) WILD-TYPE  158  167
        clus
vv       DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  FEMALE                          49                           158
  MALE                            65                           167
[1] 2 2
[1] FALSE
D28V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED   104  10
  DEL PEAK  3(1P13.1) WILD-TYPE 274  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED    104   10
  DEL PEAK  3(1P13.1) WILD-TYPE  274   49
                               clus
vv                              DEL PEAK  3(1P13.1) MUTATED
  COLON ADENOCARCINOMA                                  104
  COLON MUCINOUS ADENOCARCINOMA                          10
                               clus
vv                              DEL PEAK  3(1P13.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    274
  COLON MUCINOUS ADENOCARCINOMA                            49
[1] 2 2
[1] FALSE
D28V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.1) MUTATED     1 113
  DEL PEAK  3(1P13.1) WILD-TYPE   2 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.1) MUTATED      1  113
  DEL PEAK  3(1P13.1) WILD-TYPE    2  323
     clus
vv    DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  NO                            1                             2
  YES                         113                           323
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1P13.1) MUTATED    73   0  10   8
  DEL PEAK  3(1P13.1) WILD-TYPE 240   3  14  17
D28V10, multiclass
    clus
vv   DEL PEAK  3(1P13.1) MUTATED DEL PEAK  3(1P13.1) WILD-TYPE
  R0                          73                           240
  R1                           0                             3
  R2                          10                            14
  RX                           8                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1P13.1) MUTATED                                  1     4
  DEL PEAK  3(1P13.1) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1P13.1) MUTATED                          15    54
  DEL PEAK  3(1P13.1) WILD-TYPE                        35   157
D28V12, multiclass
                                  clus
vv                                 DEL PEAK  3(1P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     54
                                  clus
vv                                 DEL PEAK  3(1P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   35
  WHITE                                                      157
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = DEL PEAK  4(1Q43) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(1Q43) MUTATED    41   9
  DEL PEAK  4(1Q43) WILD-TYPE 294  78
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                         50                         372 
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                          9                          78 
$`DEL PEAK  4(1Q43) MUTATED`
TCGA-A6-5656 TCGA-A6-5664 TCGA-A6-6138 TCGA-AA-3519 TCGA-AA-3549 TCGA-AA-3562 
       32.91        22.09        22.52         9.07        21.01        19.99 
TCGA-AA-3673 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3867 TCGA-AA-3966 TCGA-AA-3968 
       50.04        38.99        37.02        24.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3989 TCGA-AA-A01C TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 
       16.08         7.96        15.02        41.00         0.79         1.02 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-4616 TCGA-AZ-6603 TCGA-AZ-6605 
        0.20         0.43        16.31         5.13        29.56         5.23 
TCGA-CA-5256 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5349 
        2.14        48.20         2.01         8.02        22.03        30.08 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-6531 
       29.03        13.02        15.02        11.08        10.06        17.75 
TCGA-D5-6533 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA 
        1.32        10.13         9.04        13.41        11.38         7.50 
TCGA-DM-A285 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6317 
        6.12         1.55        33.67         8.35        36.72        36.00 
TCGA-G4-6625 TCGA-NH-A50U 
       91.79        10.98 

$`DEL PEAK  4(1Q43) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        15.52        37.05        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        32.45        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        23.61        22.06        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        25.18        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       21.76        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        33.99        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       61.02        78.08         6.05         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3844 
       25.02         1.02        17.98        15.95        36.95        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       17.03         0.99        33.07        36.03        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        53.00        17.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3972 
       26.01        24.00         2.01        20.98        34.03        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       26.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 
       40.96         0.07        21.37         4.21        56.55         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        1.58         0.10         0.76         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        5.19         5.52         6.87        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       11.74         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02         8.02        26.04        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 
       13.51        11.51        20.19        20.42        18.25         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       15.58         7.53        12.39        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       28.21        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       35.93        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        46.75        47.15        52.80         4.11        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        30.28        67.00 

  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                       0.20                        0.07 
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                      91.79                      140.38 
  DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE 
                     14.215                      20.235 
[1] "0.2 - 91.8 (14.2)"  "0.1 - 140.4 (20.2)"
[1] "hr=" "1.2"
D29V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  4(1Q43) MUTATED        11        0        2        10         0
  DEL PEAK  4(1Q43) WILD-TYPE      61        1       26       121         8
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(1Q43) MUTATED           0         2          5          3
  DEL PEAK  4(1Q43) WILD-TYPE         1        19          7         52
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  4(1Q43) MUTATED            6        8         1         0
  DEL PEAK  4(1Q43) WILD-TYPE         32       35        17         2
D29V3, multiclass
            clus
vv           DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  STAGE I                           11                          61
  STAGE IA                           0                           1
  STAGE II                           2                          26
  STAGE IIA                         10                         121
  STAGE IIB                          0                           8
  STAGE IIC                          0                           1
  STAGE III                          2                          19
  STAGE IIIA                         5                           7
  STAGE IIIB                         3                          52
  STAGE IIIC                         6                          32
  STAGE IV                           8                          35
  STAGE IVA                          1                          17
  STAGE IVB                          0                           2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  4(1Q43) MUTATED     3  13  30   6
  DEL PEAK  4(1Q43) WILD-TYPE   8  63 270  45
D29V4, multiclass
    clus
vv   DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  T1                         3                           8
  T2                        13                          63
  T3                        30                         270
  T4                         6                          45
[1] 4 2
[1] 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
  DEL PEAK  4(1Q43) MUTATED    27  13  12
  DEL PEAK  4(1Q43) WILD-TYPE 229  90  67
D29V5, multiclass
    clus
vv   DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  N0                        27                         229
  N1                        13                          90
  N2                        12                          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"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK  4(1Q43) MUTATED    33   8   1   0  10
  DEL PEAK  4(1Q43) WILD-TYPE 287  44   7   2  40
D29V6, multiclass
     clus
vv    DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  M0                         33                         287
  M1                          8                          44
  M1A                         1                           7
  M1B                         0                           2
  MX                         10                          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"
D29V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q43) MUTATED    23  29
  DEL PEAK  4(1Q43) WILD-TYPE 184 203
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q43) MUTATED     23   29
  DEL PEAK  4(1Q43) WILD-TYPE  184  203
        clus
vv       DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  FEMALE                        23                         184
  MALE                          29                         203
[1] 2 2
[1] FALSE
D29V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q43) MUTATED    46   6
  DEL PEAK  4(1Q43) WILD-TYPE 332  53
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q43) MUTATED     46    6
  DEL PEAK  4(1Q43) WILD-TYPE  332   53
                               clus
vv                              DEL PEAK  4(1Q43) MUTATED
  COLON ADENOCARCINOMA                                 46
  COLON MUCINOUS ADENOCARCINOMA                         6
                               clus
vv                              DEL PEAK  4(1Q43) WILD-TYPE
  COLON ADENOCARCINOMA                                  332
  COLON MUCINOUS ADENOCARCINOMA                          53
[1] 2 2
[1] FALSE
D29V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(1Q43) MUTATED     1  51
  DEL PEAK  4(1Q43) WILD-TYPE   2 385
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(1Q43) MUTATED      1   51
  DEL PEAK  4(1Q43) WILD-TYPE    2  385
     clus
vv    DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  NO                          1                           2
  YES                        51                         385
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(1Q43) MUTATED    32   1   3   3
  DEL PEAK  4(1Q43) WILD-TYPE 281   2  21  22
D29V10, multiclass
    clus
vv   DEL PEAK  4(1Q43) MUTATED DEL PEAK  4(1Q43) WILD-TYPE
  R0                        32                         281
  R1                         1                           2
  R2                         3                          21
  RX                         3                          22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(1Q43) MUTATED                                  1     1
  DEL PEAK  4(1Q43) WILD-TYPE                                0    10
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(1Q43) MUTATED                           5    31
  DEL PEAK  4(1Q43) WILD-TYPE                        45   180
D29V12, multiclass
                                  clus
vv                                 DEL PEAK  4(1Q43) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   31
                                  clus
vv                                 DEL PEAK  4(1Q43) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                     10
  BLACK OR AFRICAN AMERICAN                                 45
  WHITE                                                    180
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = DEL PEAK  5(2P21) MUTATION ANALYSIS
D30V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  5(2P21) MUTATED    14   2
  DEL PEAK  5(2P21) WILD-TYPE 321  85
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                         16                         406 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                          2                          85 
$`DEL PEAK  5(2P21) MUTATED`
TCGA-A6-2678 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3560 TCGA-AA-3842 TCGA-AA-3939 
       42.28         1.02         6.97        19.99        37.02        12.99 
TCGA-AA-3952 TCGA-AA-A01K TCGA-AA-A01S TCGA-AZ-4313 TCGA-CM-4746 TCGA-CM-5341 
        2.01        31.00         1.02        50.37        37.02        29.06 
TCGA-D5-6534 TCGA-D5-6932 TCGA-F4-6461 TCGA-NH-A50V 
        7.92        11.38        11.11        10.52 

$`DEL PEAK  5(2P21) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       23.38        17.79        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.16        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
       37.05        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       38.99         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       26.01        12.99         0.99        14.01        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       13.02        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       54.02         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       47.01        15.02        11.01         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       36.00         5.03        85.05        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       33.07        36.03        32.05         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       53.00        17.03        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       30.02        34.03        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       27.02        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02        35.01        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       26.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        0.79         0.72         1.58         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.20         0.43         0.46         0.92        14.50        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52         6.87        75.25        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       62.79        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        3.06         2.14         3.25         3.29         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        48.20        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 
        2.93         2.01       124.27        23.05        20.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       26.04         8.02        27.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       21.99        14.99        12.99        13.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       11.01        12.95        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       11.51        20.19        20.42        17.75        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        13.38        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       61.87        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA 
       47.15        52.80         4.11        10.98         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
        6.64        14.76        30.28        67.00 

  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                       1.02                        0.07 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                      50.37                      140.38 
  DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE 
                     12.185                      19.825 
[1] "1.0 - 50.4 (12.2)"  "0.1 - 140.4 (19.8)"
[1] "hr=" "1.3"
D30V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  5(2P21) MUTATED         2        0        2         3         0
  DEL PEAK  5(2P21) WILD-TYPE      70        1       26       128         8
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2P21) MUTATED           0         1          2          2
  DEL PEAK  5(2P21) WILD-TYPE         1        20         10         53
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  5(2P21) MUTATED            4        0         0         0
  DEL PEAK  5(2P21) WILD-TYPE         34       43        18         2
D30V3, multiclass
            clus
vv           DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  STAGE I                            2                          70
  STAGE IA                           0                           1
  STAGE II                           2                          26
  STAGE IIA                          3                         128
  STAGE IIB                          0                           8
  STAGE IIC                          0                           1
  STAGE III                          1                          20
  STAGE IIIA                         2                          10
  STAGE IIIB                         2                          53
  STAGE IIIC                         4                          34
  STAGE IV                           0                          43
  STAGE IVA                          0                          18
  STAGE IVB                          0                           2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  5(2P21) MUTATED     1   3  10   2
  DEL PEAK  5(2P21) WILD-TYPE  10  73 290  49
D30V4, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  T1                         1                          10
  T2                         3                          73
  T3                        10                         290
  T4                         2                          49
[1] 4 2
[1] 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
  DEL PEAK  5(2P21) MUTATED     7   4   5
  DEL PEAK  5(2P21) WILD-TYPE 249  99  74
D30V5, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  N0                         7                         249
  N1                         4                          99
  N2                         5                          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"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK  5(2P21) MUTATED    16   0   0   0   0
  DEL PEAK  5(2P21) WILD-TYPE 304  52   8   2  50
D30V6, multiclass
     clus
vv    DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  M0                         16                         304
  M1                          0                          52
  M1A                         0                           8
  M1B                         0                           2
  MX                          0                          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"
D30V7, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED     9   7
  DEL PEAK  5(2P21) WILD-TYPE 198 225
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED      9    7
  DEL PEAK  5(2P21) WILD-TYPE  198  225
        clus
vv       DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  FEMALE                         9                         198
  MALE                           7                         225
[1] 2 2
[1] FALSE
D30V8, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED    15   1
  DEL PEAK  5(2P21) WILD-TYPE 363  58
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED     15    1
  DEL PEAK  5(2P21) WILD-TYPE  363   58
                               clus
vv                              DEL PEAK  5(2P21) MUTATED
  COLON ADENOCARCINOMA                                 15
  COLON MUCINOUS ADENOCARCINOMA                         1
                               clus
vv                              DEL PEAK  5(2P21) WILD-TYPE
  COLON ADENOCARCINOMA                                  363
  COLON MUCINOUS ADENOCARCINOMA                          58
[1] 2 2
[1] FALSE
D30V9, binary
                             cls
clus                            0   1
  DEL PEAK  5(2P21) MUTATED     0  16
  DEL PEAK  5(2P21) WILD-TYPE   3 420
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  5(2P21) MUTATED      0   16
  DEL PEAK  5(2P21) WILD-TYPE    3  420
     clus
vv    DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  NO                          0                           3
  YES                        16                         420
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  5(2P21) MUTATED    15   0   0   0
  DEL PEAK  5(2P21) WILD-TYPE 298   3  24  25
D30V10, multiclass
    clus
vv   DEL PEAK  5(2P21) MUTATED DEL PEAK  5(2P21) WILD-TYPE
  R0                        15                         298
  R1                         0                           3
  R2                         0                          24
  RX                         0                          25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2P21) MUTATED                                  0     0
  DEL PEAK  5(2P21) WILD-TYPE                                1    11
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2P21) MUTATED                           2     6
  DEL PEAK  5(2P21) WILD-TYPE                        48   205
D30V12, multiclass
                                  clus
vv                                 DEL PEAK  5(2P21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                2
  WHITE                                                    6
                                  clus
vv                                 DEL PEAK  5(2P21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     11
  BLACK OR AFRICAN AMERICAN                                 48
  WHITE                                                    205
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = DEL PEAK  6(2Q22.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q22.1) MUTATED    16   7
  DEL PEAK  6(2Q22.1) WILD-TYPE 319  80
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                           23                           399 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                            7                            80 
$`DEL PEAK  6(2Q22.1) MUTATED`
TCGA-A6-2678 TCGA-A6-3810 TCGA-A6-6651 TCGA-A6-A566 TCGA-AA-3511 TCGA-AA-3522 
       42.28        36.53        21.76        24.92         6.97        37.05 
TCGA-AA-3560 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3848 
       19.99         2.01        15.02         0.99        37.02         0.99 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AZ-4308 TCGA-CA-5254 TCGA-CA-5797 TCGA-DM-A1D6 
       12.99        24.00        75.25         2.24         3.29        49.91 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28H TCGA-F4-6704 TCGA-G4-6626 
       44.32       131.51       117.07         1.55        46.75 

$`DEL PEAK  6(2Q22.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       23.38        17.79        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 
       15.52        37.05        37.25        16.04        34.65        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.45        32.91        31.63        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       23.61        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       22.52        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        61.84        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       58.03        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
        9.07        24.03        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       29.95        23.01        20.98        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       50.04        47.05        47.01        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       19.00        36.00         5.03        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 
       15.95        38.99        36.95        14.93        17.03        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       36.03        32.05         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
        2.01        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
       34.03         2.01        21.99        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       34.06        26.01        25.02        24.00        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
        7.96        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        38.07         1.02        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       56.55         0.79         0.72         1.58         1.02         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.76         0.20         0.43         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        15.75         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52         6.87        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
      100.01        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        3.06         2.14         3.25         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       26.04         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.98        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
        1.32         7.92        15.12        17.85         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
        7.50       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
       26.47        81.37       119.93        35.97        60.79        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        91.79        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       14.76        30.28        67.00 

  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                         0.99                          0.07 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE 
                        24.00                         19.07 
[1] "1.0 - 131.5 (24.0)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.2"
D31V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  6(2Q22.1) MUTATED         0        0        1         8         0
  DEL PEAK  6(2Q22.1) WILD-TYPE      72        1       27       123         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(2Q22.1) MUTATED           0         2          1          4
  DEL PEAK  6(2Q22.1) WILD-TYPE         1        19         11         51
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  6(2Q22.1) MUTATED            5        2         1         0
  DEL PEAK  6(2Q22.1) WILD-TYPE         33       41        17         2
D31V3, multiclass
            clus
vv           DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  STAGE I                              0                            72
  STAGE IA                             0                             1
  STAGE II                             1                            27
  STAGE IIA                            8                           123
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            2                            19
  STAGE IIIA                           1                            11
  STAGE IIIB                           4                            51
  STAGE IIIC                           5                            33
  STAGE IV                             2                            41
  STAGE IVA                            1                            17
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  6(2Q22.1) MUTATED     0   1  19   4
  DEL PEAK  6(2Q22.1) WILD-TYPE  11  75 281  47
D31V4, multiclass
    clus
vv   DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  T1                           0                            11
  T2                           1                            75
  T3                          19                           281
  T4                           4                            47
[1] 4 2
[1] 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
  DEL PEAK  6(2Q22.1) MUTATED     9   8   7
  DEL PEAK  6(2Q22.1) WILD-TYPE 247  95  72
D31V5, multiclass
    clus
vv   DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  N0                           9                           247
  N1                           8                            95
  N2                           7                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  6(2Q22.1) MUTATED    19   2   1   0   2
  DEL PEAK  6(2Q22.1) WILD-TYPE 301  50   7   2  48
D31V6, multiclass
     clus
vv    DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  M0                           19                           301
  M1                            2                            50
  M1A                           1                             7
  M1B                           0                             2
  MX                            2                            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"
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q22.1) MUTATED    10  14
  DEL PEAK  6(2Q22.1) WILD-TYPE 197 218
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED     10   14
  DEL PEAK  6(2Q22.1) WILD-TYPE  197  218
        clus
vv       DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  FEMALE                          10                           197
  MALE                            14                           218
[1] 2 2
[1] FALSE
D31V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q22.1) MUTATED    21   3
  DEL PEAK  6(2Q22.1) WILD-TYPE 357  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED     21    3
  DEL PEAK  6(2Q22.1) WILD-TYPE  357   56
                               clus
vv                              DEL PEAK  6(2Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   21
  COLON MUCINOUS ADENOCARCINOMA                           3
                               clus
vv                              DEL PEAK  6(2Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    357
  COLON MUCINOUS ADENOCARCINOMA                            56
[1] 2 2
[1] FALSE
D31V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q22.1) MUTATED     0  24
  DEL PEAK  6(2Q22.1) WILD-TYPE   3 412
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q22.1) MUTATED      0   24
  DEL PEAK  6(2Q22.1) WILD-TYPE    3  412
     clus
vv    DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  NO                            0                             3
  YES                          24                           412
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q22.1) MUTATED    16   0   2   1
  DEL PEAK  6(2Q22.1) WILD-TYPE 297   3  22  24
D31V10, multiclass
    clus
vv   DEL PEAK  6(2Q22.1) MUTATED DEL PEAK  6(2Q22.1) WILD-TYPE
  R0                          16                           297
  R1                           0                             3
  R2                           2                            22
  RX                           1                            24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(2Q22.1) MUTATED                                  1     2
  DEL PEAK  6(2Q22.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(2Q22.1) MUTATED                           1     9
  DEL PEAK  6(2Q22.1) WILD-TYPE                        49   202
D31V12, multiclass
                                  clus
vv                                 DEL PEAK  6(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      9
                                  clus
vv                                 DEL PEAK  6(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   49
  WHITE                                                      202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = DEL PEAK  7(3P26.2) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P26.2) MUTATED    54  13
  DEL PEAK  7(3P26.2) WILD-TYPE 281  74
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                           67                           355 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                           13                            74 
$`DEL PEAK  7(3P26.2) MUTATED`
TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       43.43        15.52        34.65        36.53        14.53        32.45 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A5ZU TCGA-AA-3488 
       29.16        22.52        25.08        21.76         9.63         5.03 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3561 TCGA-AA-3662 
        6.97        38.99         9.07        29.00        13.94         6.05 
TCGA-AA-3679 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 
       15.02        85.05         0.99        32.05        31.07        17.03 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       29.98         2.01        12.99         2.01        21.99        50.99 
TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A01F TCGA-AA-A01K 
       24.00         7.96        13.94        27.02        32.02        31.00 
TCGA-AA-A02H TCGA-AD-A5EK TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 
        2.01         0.43         0.20         5.65         5.13        12.10 
TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 
        3.19         3.29         0.26         2.01         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 
       29.06        22.03         5.03        14.04        11.08        11.01 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        17.75         1.32         7.92        15.12        17.85 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-F4-6460 TCGA-NH-A6GA TCGA-QG-A5YV 
       13.41        11.38         7.50        13.38         5.98        26.99 
TCGA-RU-A8FL 
       30.28 

$`DEL PEAK  7(3P26.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.76        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.05        37.25        16.04        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       27.09        24.13         8.38        25.18        24.16        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        52.44         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02         1.02        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
        8.05        19.07        19.07        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       12.99         0.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       14.01         0.92        50.04        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
        5.98        37.05        19.00        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.99        33.07        36.03         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       53.00        24.03        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       33.01        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 
       16.08        13.05        34.06        26.01        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       19.07        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96        39.98         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        5.19         5.52         6.87        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
        8.02        26.04        27.02        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       11.51        20.42        18.25         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       14.30         9.04         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32        12.59       140.38        44.32       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       52.80         4.11        10.98        10.52         2.79         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        1.32         5.19         5.49        17.29         6.64        14.76 
TCGA-WS-AB45 
       67.00 

  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE 
                        13.94                         20.98 
[1] "0.2 - 85.0 (13.9)"  "0.1 - 140.4 (21.0)"
[1] "hr=" "1.4"
D32V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  7(3P26.2) MUTATED         6        0        1        19         0
  DEL PEAK  7(3P26.2) WILD-TYPE      66        1       27       112         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P26.2) MUTATED           0         4          2         11
  DEL PEAK  7(3P26.2) WILD-TYPE         1        17         10         44
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  7(3P26.2) MUTATED            8       14         4         0
  DEL PEAK  7(3P26.2) WILD-TYPE         30       29        14         2
D32V3, multiclass
            clus
vv           DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  STAGE I                              6                            66
  STAGE IA                             0                             1
  STAGE II                             1                            27
  STAGE IIA                           19                           112
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           2                            10
  STAGE IIIB                          11                            44
  STAGE IIIC                           8                            30
  STAGE IV                            14                            29
  STAGE IVA                            4                            14
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  7(3P26.2) MUTATED     2   6  51  10
  DEL PEAK  7(3P26.2) WILD-TYPE   9  70 249  41
D32V4, multiclass
    clus
vv   DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  T1                           2                             9
  T2                           6                            70
  T3                          51                           249
  T4                          10                            41
[1] 4 2
[1] 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
  DEL PEAK  7(3P26.2) MUTATED    29  21  19
  DEL PEAK  7(3P26.2) WILD-TYPE 227  82  60
D32V5, multiclass
    clus
vv   DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  N0                          29                           227
  N1                          21                            82
  N2                          19                            60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  7(3P26.2) MUTATED    42  15   3   0   8
  DEL PEAK  7(3P26.2) WILD-TYPE 278  37   5   2  42
D32V6, multiclass
     clus
vv    DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  M0                           42                           278
  M1                           15                            37
  M1A                           3                             5
  M1B                           0                             2
  MX                            8                            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"
D32V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    32  37
  DEL PEAK  7(3P26.2) WILD-TYPE 175 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     32   37
  DEL PEAK  7(3P26.2) WILD-TYPE  175  195
        clus
vv       DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  FEMALE                          32                           175
  MALE                            37                           195
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED    65   4
  DEL PEAK  7(3P26.2) WILD-TYPE 313  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED     65    4
  DEL PEAK  7(3P26.2) WILD-TYPE  313   55
                               clus
vv                              DEL PEAK  7(3P26.2) MUTATED
  COLON ADENOCARCINOMA                                   65
  COLON MUCINOUS ADENOCARCINOMA                           4
                               clus
vv                              DEL PEAK  7(3P26.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    313
  COLON MUCINOUS ADENOCARCINOMA                            55
[1] 2 2
[1] FALSE
D32V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.2) MUTATED     0  69
  DEL PEAK  7(3P26.2) WILD-TYPE   3 367
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.2) MUTATED      0   69
  DEL PEAK  7(3P26.2) WILD-TYPE    3  367
     clus
vv    DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  NO                            0                             3
  YES                          69                           367
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(3P26.2) MUTATED    49   0   7   4
  DEL PEAK  7(3P26.2) WILD-TYPE 264   3  17  21
D32V10, multiclass
    clus
vv   DEL PEAK  7(3P26.2) MUTATED DEL PEAK  7(3P26.2) WILD-TYPE
  R0                          49                           264
  R1                           0                             3
  R2                           7                            17
  RX                           4                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3P26.2) MUTATED                                  0     2
  DEL PEAK  7(3P26.2) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P26.2) MUTATED                           7    32
  DEL PEAK  7(3P26.2) WILD-TYPE                        43   179
D32V12, multiclass
                                  clus
vv                                 DEL PEAK  7(3P26.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     32
                                  clus
vv                                 DEL PEAK  7(3P26.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   43
  WHITE                                                      179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK  8(3P14.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P14.2) MUTATED    66  16
  DEL PEAK  8(3P14.2) WILD-TYPE 269  71
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           82                           340 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           16                            71 
$`DEL PEAK  8(3P14.2) MUTATED`
TCGA-4T-AA8H TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
        5.26        15.52        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 
       32.45        29.16        22.52        25.08        21.76        20.12 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       52.44         9.63         5.03        38.99         1.02         9.07 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3697 
        6.05        54.02         0.92        11.01        37.05        85.05 
TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3939 
        0.99        32.05        31.07        17.03         2.01        12.99 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
        2.01        21.99        24.00        27.02         7.96        13.94 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A01F TCGA-AA-A01K 
       18.05        17.03        27.02         0.99        32.02        31.00 
TCGA-AA-A02W TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 
       41.00        21.37         0.79         1.58         0.43         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-6600 
       14.50        16.31         0.20        75.25         5.65        12.10 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 
        3.29         0.26         2.01         8.02         5.03        14.04 
TCGA-CM-6171 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       14.04        13.05        11.08        11.01        20.19        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 
        1.32         7.92        17.85        13.41        11.38       119.70 
TCGA-DM-A1DA TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-G4-6317 TCGA-NH-A6GA 
        7.50        35.97       117.07        13.38        36.00         5.98 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-RU-A8FL TCGA-WS-AB45 
        5.49        26.99        30.28        67.00 

$`DEL PEAK  8(3P14.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06        37.02        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       37.05        37.25        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.18        24.16        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       61.84         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       34.03        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       14.01        33.99        21.01        13.02        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       29.95        23.01        20.98        19.99        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.05        47.01        15.02         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
        0.99        31.07        53.00        24.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       18.05        31.00        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 
        2.01        20.98        34.03        16.08        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       34.06        26.01        25.02        19.07        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05         4.01        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
        0.99        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
        1.02        33.04        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       51.98         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 
       22.03        39.98        18.05        40.96         0.07         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.72         1.02         0.10         0.76         0.20 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52         6.87        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       61.41        49.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       11.74         3.19         1.94         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02         8.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       12.95        11.08        10.06        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 
       19.59        13.51        11.51        20.42        18.25        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
       11.64         1.51        12.00        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K 
       14.04        26.47        81.37       119.93        60.79        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
        4.11        10.98        10.52         2.79         5.59         1.32 
TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19        17.29         6.64        14.76 

  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                       119.70                        140.38 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                       14.515                        20.995 
[1] "0.2 - 119.7 (14.5)" "0.1 - 140.4 (21.0)"
[1] "hr=" "1.1"
D33V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  8(3P14.2) MUTATED        10        0        2        24         0
  DEL PEAK  8(3P14.2) WILD-TYPE      62        1       26       107         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P14.2) MUTATED           0         5          1         14
  DEL PEAK  8(3P14.2) WILD-TYPE         1        16         11         41
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  8(3P14.2) MUTATED           11       11         5         1
  DEL PEAK  8(3P14.2) WILD-TYPE         27       32        13         1
D33V3, multiclass
            clus
vv           DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  STAGE I                             10                            62
  STAGE IA                             0                             1
  STAGE II                             2                            26
  STAGE IIA                           24                           107
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           1                            11
  STAGE IIIB                          14                            41
  STAGE IIIC                          11                            27
  STAGE IV                            11                            32
  STAGE IVA                            5                            13
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  8(3P14.2) MUTATED     3   9  59  14
  DEL PEAK  8(3P14.2) WILD-TYPE   8  67 241  37
D33V4, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  T1                           3                             8
  T2                           9                            67
  T3                          59                           241
  T4                          14                            37
[1] 4 2
[1] 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
  DEL PEAK  8(3P14.2) MUTATED    40  23  22
  DEL PEAK  8(3P14.2) WILD-TYPE 216  80  57
D33V5, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  N0                          40                           216
  N1                          23                            80
  N2                          22                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  8(3P14.2) MUTATED    55  13   3   1  12
  DEL PEAK  8(3P14.2) WILD-TYPE 265  39   5   1  38
D33V6, multiclass
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  M0                           55                           265
  M1                           13                            39
  M1A                           3                             5
  M1B                           1                             1
  MX                           12                            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"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    43  42
  DEL PEAK  8(3P14.2) WILD-TYPE 164 190
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     43   42
  DEL PEAK  8(3P14.2) WILD-TYPE  164  190
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  FEMALE                          43                           164
  MALE                            42                           190
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    76   9
  DEL PEAK  8(3P14.2) WILD-TYPE 302  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     76    9
  DEL PEAK  8(3P14.2) WILD-TYPE  302   50
                               clus
vv                              DEL PEAK  8(3P14.2) MUTATED
  COLON ADENOCARCINOMA                                   76
  COLON MUCINOUS ADENOCARCINOMA                           9
                               clus
vv                              DEL PEAK  8(3P14.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    302
  COLON MUCINOUS ADENOCARCINOMA                            50
[1] 2 2
[1] FALSE
D33V9, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED     0  85
  DEL PEAK  8(3P14.2) WILD-TYPE   3 351
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED      0   85
  DEL PEAK  8(3P14.2) WILD-TYPE    3  351
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  NO                            0                             3
  YES                          85                           351
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P14.2) MUTATED    60   1   6   4
  DEL PEAK  8(3P14.2) WILD-TYPE 253   2  18  21
D33V10, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  R0                          60                           253
  R1                           1                             2
  R2                           6                            18
  RX                           4                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(3P14.2) MUTATED                                  0     2
  DEL PEAK  8(3P14.2) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P14.2) MUTATED                          12    39
  DEL PEAK  8(3P14.2) WILD-TYPE                        38   172
D33V12, multiclass
                                  clus
vv                                 DEL PEAK  8(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     39
                                  clus
vv                                 DEL PEAK  8(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      172
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = DEL PEAK  9(3Q26.31) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  9(3Q26.31) MUTATED    34   9
  DEL PEAK  9(3Q26.31) WILD-TYPE 301  78
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            43                            379 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                             9                             78 
$`DEL PEAK  9(3Q26.31) MUTATED`
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-4105 TCGA-A6-4107 TCGA-AA-3517 TCGA-AA-3662 
       15.52        37.25        14.53        32.45        38.99         6.05 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 
       85.05         0.99        32.05        12.99         2.01        21.99 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A01F TCGA-AA-A01T TCGA-AD-6548 
        7.96        13.94        27.02        32.02        33.04        21.37 
TCGA-AD-6899 TCGA-AD-A5EK TCGA-AY-5543 TCGA-AZ-6600 TCGA-CA-6716 TCGA-CM-4752 
        1.58         0.43        15.75        12.10         0.26        13.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5540 TCGA-D5-6529 
       15.02         5.03        11.08        11.01        13.51        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
        1.32         7.92        17.85        13.41        12.00        11.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F TCGA-G4-6297 TCGA-G4-6317 TCGA-QG-A5YV 
        7.50       131.51        35.97        82.39        36.00        26.99 
TCGA-RU-A8FL 
       30.28 

$`DEL PEAK  9(3Q26.31) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       13.94        37.05        16.04        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.06        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
        8.38        25.08        25.18        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       24.69        24.39        23.87        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       58.03        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        9.07        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        34.03        29.00        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
        0.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       11.01         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       14.93        17.03         0.99        33.07        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       31.07        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        19.07        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q 
       34.03        18.05        18.05        17.03         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02         0.99        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
        0.07         4.21        56.55         0.79         0.72         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         0.20         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
        5.19         5.52         6.87        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        1.41         5.65        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       65.00        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
        3.06         2.14         3.25         3.29         0.07         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04         8.02        27.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        10.06        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 
       19.59        11.51        20.42        17.75        18.25        15.12 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       11.64         1.51        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
       44.32       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       28.21         8.35        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        1.32         5.19         5.49        17.29         6.64        14.76 
TCGA-WS-AB45 
       67.00 

  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                          0.26                           0.07 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                         14.53                          20.12 
[1] "0.3 - 131.5 (14.5)" "0.1 - 140.4 (20.1)"
[1] "hr=" "1.2"
D34V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  9(3Q26.31) MUTATED         4        0        0        15         0
  DEL PEAK  9(3Q26.31) WILD-TYPE      68        1       28       116         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3Q26.31) MUTATED           0         3          0          5
  DEL PEAK  9(3Q26.31) WILD-TYPE         1        18         12         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  9(3Q26.31) MUTATED            8        6         3         0
  DEL PEAK  9(3Q26.31) WILD-TYPE         30       37        15         2
D34V3, multiclass
            clus
vv           DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  STAGE I                               4                             68
  STAGE IA                              0                              1
  STAGE II                              0                             28
  STAGE IIA                            15                            116
  STAGE IIB                             0                              8
  STAGE IIC                             0                              1
  STAGE III                             3                             18
  STAGE IIIA                            0                             12
  STAGE IIIB                            5                             50
  STAGE IIIC                            8                             30
  STAGE IV                              6                             37
  STAGE IVA                             3                             15
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  9(3Q26.31) MUTATED     0   4  32   8
  DEL PEAK  9(3Q26.31) WILD-TYPE  11  72 268  43
D34V4, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  T1                            0                             11
  T2                            4                             72
  T3                           32                            268
  T4                            8                             43
[1] 4 2
[1] 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
  DEL PEAK  9(3Q26.31) MUTATED    22  10  12
  DEL PEAK  9(3Q26.31) WILD-TYPE 234  93  67
D34V5, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  N0                           22                            234
  N1                           10                             93
  N2                           12                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK  9(3Q26.31) MUTATED    30   7   2   0   5
  DEL PEAK  9(3Q26.31) WILD-TYPE 290  45   6   2  45
D34V6, multiclass
     clus
vv    DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  M0                            30                            290
  M1                             7                             45
  M1A                            2                              6
  M1B                            0                              2
  MX                             5                             45
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED    22  22
  DEL PEAK  9(3Q26.31) WILD-TYPE 185 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED     22   22
  DEL PEAK  9(3Q26.31) WILD-TYPE  185  210
        clus
vv       DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  FEMALE                           22                            185
  MALE                             22                            210
[1] 2 2
[1] FALSE
D34V8, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED    41   3
  DEL PEAK  9(3Q26.31) WILD-TYPE 337  56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED     41    3
  DEL PEAK  9(3Q26.31) WILD-TYPE  337   56
                               clus
vv                              DEL PEAK  9(3Q26.31) MUTATED
  COLON ADENOCARCINOMA                                    41
  COLON MUCINOUS ADENOCARCINOMA                            3
                               clus
vv                              DEL PEAK  9(3Q26.31) WILD-TYPE
  COLON ADENOCARCINOMA                                     337
  COLON MUCINOUS ADENOCARCINOMA                             56
[1] 2 2
[1] FALSE
D34V9, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED     0  44
  DEL PEAK  9(3Q26.31) WILD-TYPE   3 392
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED      0   44
  DEL PEAK  9(3Q26.31) WILD-TYPE    3  392
     clus
vv    DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  NO                             0                              3
  YES                           44                            392
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  9(3Q26.31) MUTATED    34   0   2   1
  DEL PEAK  9(3Q26.31) WILD-TYPE 279   3  22  24
D34V10, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  R0                           34                            279
  R1                            0                              3
  R2                            2                             22
  RX                            1                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(3Q26.31) MUTATED                                  0     1
  DEL PEAK  9(3Q26.31) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3Q26.31) MUTATED                           7    22
  DEL PEAK  9(3Q26.31) WILD-TYPE                        43   189
D34V12, multiclass
                                  clus
vv                                 DEL PEAK  9(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      22
                                  clus
vv                                 DEL PEAK  9(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    43
  WHITE                                                       189
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK 10(4P16.2) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4P16.2) MUTATED    91  34
  DEL PEAK 10(4P16.2) WILD-TYPE 244  53
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                          125                           297 
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                           34                            53 
$`DEL PEAK 10(4P16.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       37.02        43.76        44.91        35.11        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 
       37.05        16.04        14.53        32.45        30.44        29.16 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       25.18        21.76        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 
        9.63         5.03         1.02        38.99        37.05        34.03 
TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3664 
       12.99        21.01        13.02        19.99         6.05        54.02 
TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 
        2.01        50.04        15.02        36.00        85.05        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       36.95        37.02        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
        0.99        31.07        31.07        53.00        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 
       29.98         2.01        12.99         2.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C 
       21.99        50.99        26.01        34.03        42.02        15.02 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       32.02        31.00        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 
        2.01        41.00         1.58         1.02         0.20        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 
        0.95        15.75         0.20         5.52         5.65         5.13 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5797 
       65.00        12.10        29.56         3.19         2.14         3.29 
TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5864 
       48.20         8.02        29.06        22.03        22.98        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6677 
       17.03        14.04        29.03        13.02        15.02        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 
       11.01        10.06        14.99        13.51        20.19        17.75 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA 
       14.30         9.04        13.41        11.38        12.59         7.50 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 
        6.12        14.04        26.47         1.55        16.24        33.67 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 
       35.41         8.35        23.51        45.11        36.72        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A8F8 TCGA-QG-A5YV 
       46.75         4.11        10.98         5.49        26.99 

$`DEL PEAK 10(4P16.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       42.28        45.60        37.25        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       16.24        24.92         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 
       35.01        58.03        63.98         6.97         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        24.03        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
       19.07        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3667 
       19.99        13.94        61.02        78.08         6.97        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
        0.92        47.05        47.01        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       19.00         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       14.93        36.03        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       33.01        26.01        24.00        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        17.03         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       14.99        21.99        34.98        15.02         0.99        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       37.02        39.06        51.98         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
       56.55         0.79         0.72         0.10         0.76         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 
        0.46         0.92        27.09        16.31        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
        6.77       100.01         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         0.07         0.26         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
       23.05        20.02        37.02         8.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       13.02        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 
       14.04        11.01        12.95        13.05        11.08        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       12.26        19.59        11.51        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        7.92        15.12        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       24.43        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 
        6.18        35.87        16.31        29.59         1.28         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       19.43       107.67        28.21        82.39        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80        10.52         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.98         5.59         1.32         5.19        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       14.76        30.28        67.00 

  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                        91.79                        140.38 
  DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE 
                        17.75                         19.66 
[1] "0.2 - 91.8 (17.8)"  "0.1 - 140.4 (19.7)"
[1] "hr=" "1.8"
D35V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 10(4P16.2) MUTATED        15        0        6        30         2
  DEL PEAK 10(4P16.2) WILD-TYPE      57        1       22       101         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(4P16.2) MUTATED           0         5          6         14
  DEL PEAK 10(4P16.2) WILD-TYPE         1        16          6         41
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 10(4P16.2) MUTATED           15       26         7         0
  DEL PEAK 10(4P16.2) WILD-TYPE         23       17        11         2
D35V3, multiclass
            clus
vv           DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  STAGE I                             15                            57
  STAGE IA                             0                             1
  STAGE II                             6                            22
  STAGE IIA                           30                           101
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           6                             6
  STAGE IIIB                          14                            41
  STAGE IIIC                          15                            23
  STAGE IV                            26                            17
  STAGE IVA                            7                            11
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 10(4P16.2) MUTATED     4  19  88  19
  DEL PEAK 10(4P16.2) WILD-TYPE   7  57 212  32
D35V4, multiclass
    clus
vv   DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  T1                           4                             7
  T2                          19                            57
  T3                          88                           212
  T4                          19                            32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 10(4P16.2) MUTATED    58  38  34
  DEL PEAK 10(4P16.2) WILD-TYPE 198  65  45
D35V5, multiclass
    clus
vv   DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  N0                          58                           198
  N1                          38                            65
  N2                          34                            45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 10(4P16.2) MUTATED    79  29   4   0  14
  DEL PEAK 10(4P16.2) WILD-TYPE 241  23   4   2  36
D35V6, multiclass
     clus
vv    DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  M0                           79                           241
  M1                           29                            23
  M1A                           4                             4
  M1B                           0                             2
  MX                           14                            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"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.2) MUTATED    58  72
  DEL PEAK 10(4P16.2) WILD-TYPE 149 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.2) MUTATED     58   72
  DEL PEAK 10(4P16.2) WILD-TYPE  149  160
        clus
vv       DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  FEMALE                          58                           149
  MALE                            72                           160
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.2) MUTATED   119  10
  DEL PEAK 10(4P16.2) WILD-TYPE 259  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.2) MUTATED    119   10
  DEL PEAK 10(4P16.2) WILD-TYPE  259   49
                               clus
vv                              DEL PEAK 10(4P16.2) MUTATED
  COLON ADENOCARCINOMA                                  119
  COLON MUCINOUS ADENOCARCINOMA                          10
                               clus
vv                              DEL PEAK 10(4P16.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    259
  COLON MUCINOUS ADENOCARCINOMA                            49
[1] 2 2
[1] FALSE
D35V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.2) MUTATED     3 127
  DEL PEAK 10(4P16.2) WILD-TYPE   0 309
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.2) MUTATED      3  127
  DEL PEAK 10(4P16.2) WILD-TYPE    0  309
     clus
vv    DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  NO                            3                             0
  YES                         127                           309
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4P16.2) MUTATED    91   0  13   5
  DEL PEAK 10(4P16.2) WILD-TYPE 222   3  11  20
D35V10, multiclass
    clus
vv   DEL PEAK 10(4P16.2) MUTATED DEL PEAK 10(4P16.2) WILD-TYPE
  R0                          91                           222
  R1                           0                             3
  R2                          13                            11
  RX                           5                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(4P16.2) MUTATED                                  1     2
  DEL PEAK 10(4P16.2) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4P16.2) MUTATED                          13    61
  DEL PEAK 10(4P16.2) WILD-TYPE                        37   150
D35V12, multiclass
                                  clus
vv                                 DEL PEAK 10(4P16.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                     61
                                  clus
vv                                 DEL PEAK 10(4P16.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   37
  WHITE                                                      150
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK 11(4Q22.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q22.1) MUTATED   103  35
  DEL PEAK 11(4Q22.1) WILD-TYPE 232  52
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          138                           284 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                           35                            52 
$`DEL PEAK 11(4Q22.1) MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 
       43.76        43.43        44.91        35.11        13.94        15.52 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       37.05        34.65        36.53        32.45        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       29.16        24.16        21.76        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3511 
       52.44         9.63         5.03         1.02        63.98         6.97 
TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3548 TCGA-AA-3549 
       38.99        37.05        34.03        29.00        33.99        21.01 
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 
       13.02        19.99         6.05         2.01        50.04        37.05 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00         0.99         0.99        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 
       17.03         0.99        33.07         0.99        31.07        17.03 
TCGA-AA-3930 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
        2.01         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q 
       50.99        26.01        24.00        27.02        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       17.03        15.02        32.02        26.01         2.96        39.98 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 
       41.00         1.58         1.02         0.20        14.50        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-4681 
        0.95         0.20         5.52         6.87         5.13        83.80 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 
       65.00        12.10        29.56         2.14         3.29         1.35 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
      102.44        48.20         8.02        13.02        29.06        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
        5.03        15.02        17.03        14.04        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 
       15.02        11.01        13.05        11.08        11.01        14.99 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       13.51        20.19        17.75         1.32         7.92        15.12 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD 
       14.30         9.04        13.41        12.00        11.38        24.43 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F 
       12.59         7.50        44.32         6.12        14.04        35.97 
TCGA-F4-6460 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 
       13.38        16.24        33.67        35.41        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 
       82.39        23.51        45.11        36.72        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-RU-A8FL 
        4.11        10.98         5.98         5.49        26.99        30.28 

$`DEL PEAK 11(4Q22.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        37.02        46.65        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5656 
       42.28        45.60        37.25        16.04        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       20.61        24.69        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       24.92         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       58.03         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3538 
       36.03         8.05        19.07        19.07        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       12.99         0.99        14.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       15.02        11.01         5.98        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        19.04        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
       17.98        15.95        14.93        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3971 
       12.99        24.00        33.01        26.01        24.00        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
       17.03         4.01        27.02         0.99        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02         0.99        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        39.06        51.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         0.10         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 
        0.43         0.46         0.92        27.09        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82         5.19        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.65        32.94        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        6.77       100.01         5.23        11.74         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.06         3.25         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        0.10        17.56        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       20.02        37.02         8.02        26.04        27.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 
       30.08        16.01        15.02        15.02        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       16.04        21.99        14.99        12.99        14.04        12.95 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       11.08        10.06        12.03        12.26        19.59        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       20.42        18.25        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        9.44        11.64         1.51        10.26       119.70        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA 
      130.65        92.75        49.91        13.32       140.38       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       29.59         1.28         0.53        19.43       107.67        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        35.93        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       13.78        35.80        26.17        47.15        52.80        10.52 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 
        2.79         5.59         1.32         5.19        17.29         6.64 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       14.76        67.00 

  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                       102.44                        140.38 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                       18.870                        19.625 
[1] "0.2 - 102.4 (18.9)" "0.1 - 140.4 (19.6)"
[1] "hr=" "1.6"
D36V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 11(4Q22.1) MUTATED        13        0        8        37         2
  DEL PEAK 11(4Q22.1) WILD-TYPE      59        1       20        94         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4Q22.1) MUTATED           0         3          7         22
  DEL PEAK 11(4Q22.1) WILD-TYPE         1        18          5         33
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 11(4Q22.1) MUTATED           18       21         6         1
  DEL PEAK 11(4Q22.1) WILD-TYPE         20       22        12         1
D36V3, multiclass
            clus
vv           DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  STAGE I                             13                            59
  STAGE IA                             0                             1
  STAGE II                             8                            20
  STAGE IIA                           37                            94
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           7                             5
  STAGE IIIB                          22                            33
  STAGE IIIC                          18                            20
  STAGE IV                            21                            22
  STAGE IVA                            6                            12
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 11(4Q22.1) MUTATED     4  17 101  20
  DEL PEAK 11(4Q22.1) WILD-TYPE   7  59 199  31
D36V4, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  T1                           4                             7
  T2                          17                            59
  T3                         101                           199
  T4                          20                            31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 11(4Q22.1) MUTATED    64  43  35
  DEL PEAK 11(4Q22.1) WILD-TYPE 192  60  44
D36V5, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  N0                          64                           192
  N1                          43                            60
  N2                          35                            44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 11(4Q22.1) MUTATED    93  23   4   1  17
  DEL PEAK 11(4Q22.1) WILD-TYPE 227  29   4   1  33
D36V6, multiclass
     clus
vv    DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  M0                           93                           227
  M1                           23                            29
  M1A                           4                             4
  M1B                           1                             1
  MX                           17                            33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED    62  80
  DEL PEAK 11(4Q22.1) WILD-TYPE 145 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED     62   80
  DEL PEAK 11(4Q22.1) WILD-TYPE  145  152
        clus
vv       DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  FEMALE                          62                           145
  MALE                            80                           152
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED   131  10
  DEL PEAK 11(4Q22.1) WILD-TYPE 247  49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED    131   10
  DEL PEAK 11(4Q22.1) WILD-TYPE  247   49
                               clus
vv                              DEL PEAK 11(4Q22.1) MUTATED
  COLON ADENOCARCINOMA                                  131
  COLON MUCINOUS ADENOCARCINOMA                          10
                               clus
vv                              DEL PEAK 11(4Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    247
  COLON MUCINOUS ADENOCARCINOMA                            49
[1] 2 2
[1] FALSE
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED     3 139
  DEL PEAK 11(4Q22.1) WILD-TYPE   0 297
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED      3  139
  DEL PEAK 11(4Q22.1) WILD-TYPE    0  297
     clus
vv    DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  NO                            3                             0
  YES                         139                           297
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q22.1) MUTATED   102   1   9   7
  DEL PEAK 11(4Q22.1) WILD-TYPE 211   2  15  18
D36V10, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  R0                         102                           211
  R1                           1                             2
  R2                           9                            15
  RX                           7                            18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(4Q22.1) MUTATED                                  0     3
  DEL PEAK 11(4Q22.1) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4Q22.1) MUTATED                          19    70
  DEL PEAK 11(4Q22.1) WILD-TYPE                        31   141
D36V12, multiclass
                                  clus
vv                                 DEL PEAK 11(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                     70
                                  clus
vv                                 DEL PEAK 11(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      141
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK 12(4Q35.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4Q35.1) MUTATED   114  32
  DEL PEAK 12(4Q35.1) WILD-TYPE 221  55
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          146                           276 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                           32                            55 
$`DEL PEAK 12(4Q35.1) MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       43.76        43.43        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 
       37.05        37.25        34.65        32.45        29.19        29.16 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 
       24.13        25.08        24.16        20.61        21.76        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       20.28        61.84        52.44         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 
       38.99        37.05        34.03        29.00        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       33.99        21.01        13.02        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 
       54.02         2.01        50.04        37.05        36.00        85.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
        0.99        38.99        36.95        37.02        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 
       33.07        36.03         0.99        31.07        17.03         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q 
       26.01        24.00         7.96        34.03        17.03        42.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01X 
       15.02        32.02        31.00        35.01         1.02        26.01 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 
        2.96        39.98         2.01        41.00         1.02         0.20 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 
       14.50        16.31         0.95         5.52        75.25         5.65 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-5256 
        5.13        65.00        12.10        29.56         2.24         2.14 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
        0.10         1.35        48.20         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.03        30.08         5.03        15.02        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 
       14.04        29.03        13.02        15.02        11.01        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       11.01        14.99        13.51        20.19        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D7 
        7.92        17.85         7.53         9.04        13.41        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 
      140.38         7.50        44.32       131.51         6.12        14.04 
TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 
       26.47        13.38         1.55        16.24        33.67        35.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 
        8.35        82.39        23.51        45.11        36.72        91.79 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 
       46.75         4.11        10.98         5.98         1.32         5.49 
TCGA-QG-A5YV TCGA-RU-A8FL 
       26.99        30.28 

$`DEL PEAK 12(4Q35.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        37.02        46.65        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       42.28        44.91        16.04        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        30.44        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 
       32.71        27.09        22.52         8.38        25.18        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 
       24.39        20.12        19.66        16.24        24.92         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3542 
       36.03         8.05        19.07        19.07        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
        0.99        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 
       19.99        13.94        61.02         6.97        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 
       47.05        47.01        15.02        11.01         5.98        19.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 
        5.03        26.99        19.04         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3855 
       25.02         1.02        17.98        15.95        14.93        32.05 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        24.03        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00        12.99        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
        2.01        13.05        34.06        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        15.02         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       38.07         1.02        33.04        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       51.98         5.03         0.92        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.72         1.58         0.10         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        5.19         6.87        50.37        58.39         1.41        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       83.80        22.36        62.79        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 
      100.01         5.23        11.74         3.19         1.94         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 
        3.25         3.29         0.07         0.26         0.33        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 
       37.02         8.02        26.04        27.02        22.98        16.01 
TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       12.99        14.04        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       12.03        12.26        19.59        11.51        20.42        18.25 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1HB 
       38.20       130.65        92.75        49.91        12.59       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
        7.76       139.17        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 
       13.45         6.18        35.87        16.31        29.59         1.28 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 
        0.53        19.43       107.67        28.21        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80        10.52         2.79 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.59         5.19        17.29         6.64        14.76        67.00 

  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                       20.445                        19.070 
[1] "0.1 - 140.4 (20.4)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1.2"
D37V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 12(4Q35.1) MUTATED        16        0        7        42         1
  DEL PEAK 12(4Q35.1) WILD-TYPE      56        1       21        89         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q35.1) MUTATED           0         7          6         20
  DEL PEAK 12(4Q35.1) WILD-TYPE         1        14          6         35
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 12(4Q35.1) MUTATED           17       23         7         1
  DEL PEAK 12(4Q35.1) WILD-TYPE         21       20        11         1
D37V3, multiclass
            clus
vv           DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  STAGE I                             16                            56
  STAGE IA                             0                             1
  STAGE II                             7                            21
  STAGE IIA                           42                            89
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            7                            14
  STAGE IIIA                           6                             6
  STAGE IIIB                          20                            35
  STAGE IIIC                          17                            21
  STAGE IV                            23                            20
  STAGE IVA                            7                            11
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 12(4Q35.1) MUTATED     4  20 105  21
  DEL PEAK 12(4Q35.1) WILD-TYPE   7  56 195  30
D37V4, multiclass
    clus
vv   DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  T1                           4                             7
  T2                          20                            56
  T3                         105                           195
  T4                          21                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 12(4Q35.1) MUTATED    71  43  36
  DEL PEAK 12(4Q35.1) WILD-TYPE 185  60  43
D37V5, multiclass
    clus
vv   DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  N0                          71                           185
  N1                          43                            60
  N2                          36                            43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 12(4Q35.1) MUTATED   102  25   5   1  16
  DEL PEAK 12(4Q35.1) WILD-TYPE 218  27   3   1  34
D37V6, multiclass
     clus
vv    DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  M0                          102                           218
  M1                           25                            27
  M1A                           5                             3
  M1B                           1                             1
  MX                           16                            34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED    76  74
  DEL PEAK 12(4Q35.1) WILD-TYPE 131 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED     76   74
  DEL PEAK 12(4Q35.1) WILD-TYPE  131  158
        clus
vv       DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  FEMALE                          76                           131
  MALE                            74                           158
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED   135  14
  DEL PEAK 12(4Q35.1) WILD-TYPE 243  45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED    135   14
  DEL PEAK 12(4Q35.1) WILD-TYPE  243   45
                               clus
vv                              DEL PEAK 12(4Q35.1) MUTATED
  COLON ADENOCARCINOMA                                  135
  COLON MUCINOUS ADENOCARCINOMA                          14
                               clus
vv                              DEL PEAK 12(4Q35.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    243
  COLON MUCINOUS ADENOCARCINOMA                            45
[1] 2 2
[1] FALSE
D37V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED     3 147
  DEL PEAK 12(4Q35.1) WILD-TYPE   0 289
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED      3  147
  DEL PEAK 12(4Q35.1) WILD-TYPE    0  289
     clus
vv    DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  NO                            3                             0
  YES                         147                           289
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q35.1) MUTATED   104   1  12   8
  DEL PEAK 12(4Q35.1) WILD-TYPE 209   2  12  17
D37V10, multiclass
    clus
vv   DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  R0                         104                           209
  R1                           1                             2
  R2                          12                            12
  RX                           8                            17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(4Q35.1) MUTATED                                  1     4
  DEL PEAK 12(4Q35.1) WILD-TYPE                                0     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4Q35.1) MUTATED                          20    68
  DEL PEAK 12(4Q35.1) WILD-TYPE                        30   143
D37V12, multiclass
                                  clus
vv                                 DEL PEAK 12(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 20
  WHITE                                                     68
                                  clus
vv                                 DEL PEAK 12(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   30
  WHITE                                                      143
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = DEL PEAK 13(5Q12.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q12.1) MUTATED    72  26
  DEL PEAK 13(5Q12.1) WILD-TYPE 263  61
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                           98                           324 
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                           26                            61 
$`DEL PEAK 13(5Q12.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2683 
       37.02        43.76        43.43        23.38        13.94        15.52 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 
       16.04        34.65        36.53        14.53        30.44        29.19 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09        25.08        25.18        24.16        21.76        24.69 
TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3502 TCGA-AA-3538 TCGA-AA-3542 
       23.87         9.63         5.03        35.01        26.01        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 
       13.02        24.00        19.99        50.04        47.01        37.05 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3851 
       19.00        85.05         0.99        36.95        37.02        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3966 
        0.99        31.07        31.07        24.03         2.01         2.01 
TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T 
       21.99        34.03        27.02        42.02         0.99        33.04 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        2.96         2.01        41.00         1.02         0.10         0.20 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
       16.31         0.20         5.65        65.00        62.79        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4747 
        5.23         1.94         3.29         1.35        48.20         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
        8.02        13.02        29.06        22.03         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6898 
       14.04        29.03        13.02        17.75        17.85         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 
       10.13        12.43         9.04        44.32       131.51         6.12 
TCGA-F4-6459 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 
        8.61         1.55        33.67         8.35        82.39        45.11 
TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV 
       36.00        91.79         4.11        10.98         1.32        26.99 
TCGA-QG-A5Z1 TCGA-RU-A8FL 
        6.64        30.28 

$`DEL PEAK 13(5Q12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
        5.06         5.26        46.65        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 
       35.11        45.60        37.05        37.25        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6653 
       29.16        22.52        24.13         8.38        20.61        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       52.44         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 
       19.07        19.07        34.03        29.00        29.00         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        33.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       20.98        19.99        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.97        54.02         2.01        14.01         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       15.02        11.01         5.98        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        14.93        17.03         0.99 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 
       36.03        32.05        53.00        17.03        27.02        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 
       18.05        31.00         2.01        12.99        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 
       26.01        24.00        20.98        34.03        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        17.03         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72         1.58         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.92        14.50        27.09         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 
       17.82         5.19         5.52         6.87        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41        32.94         5.13        83.80        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        3.19         2.24         3.06         2.14         3.25         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        2.01       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       27.02        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        13.51        11.51        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        15.12         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 
       12.49        16.14        15.58        12.39        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
       13.32        12.59       140.38         7.50       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24        95.18        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       28.21        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        51.75        39.42        35.93        36.72 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        47.15        52.80        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.59         5.19         5.49        17.29        14.76        67.00 

  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE 
                       21.875                        19.250 
[1] "0.1 - 131.5 (21.9)" "0.1 - 140.4 (19.2)"
[1] "hr=" "1.5"
D38V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 13(5Q12.1) MUTATED        14        0        4        18         1
  DEL PEAK 13(5Q12.1) WILD-TYPE      58        1       24       113         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(5Q12.1) MUTATED           0         4          6         13
  DEL PEAK 13(5Q12.1) WILD-TYPE         1        17          6         42
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 13(5Q12.1) MUTATED           15       12         8         1
  DEL PEAK 13(5Q12.1) WILD-TYPE         23       31        10         1
D38V3, multiclass
            clus
vv           DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  STAGE I                             14                            58
  STAGE IA                             0                             1
  STAGE II                             4                            24
  STAGE IIA                           18                           113
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           6                             6
  STAGE IIIB                          13                            42
  STAGE IIIC                          15                            23
  STAGE IV                            12                            31
  STAGE IVA                            8                            10
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 13(5Q12.1) MUTATED     3  17  67  13
  DEL PEAK 13(5Q12.1) WILD-TYPE   8  59 233  38
D38V4, multiclass
    clus
vv   DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  T1                           3                             8
  T2                          17                            59
  T3                          67                           233
  T4                          13                            38
[1] 4 2
[1] 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
  DEL PEAK 13(5Q12.1) MUTATED    44  29  27
  DEL PEAK 13(5Q12.1) WILD-TYPE 212  74  52
D38V5, multiclass
    clus
vv   DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  N0                          44                           212
  N1                          29                            74
  N2                          27                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 13(5Q12.1) MUTATED    63  15   5   1  15
  DEL PEAK 13(5Q12.1) WILD-TYPE 257  37   3   1  35
D38V6, multiclass
     clus
vv    DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  M0                           63                           257
  M1                           15                            37
  M1A                           5                             3
  M1B                           1                             1
  MX                           15                            35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q12.1) MUTATED    41  59
  DEL PEAK 13(5Q12.1) WILD-TYPE 166 173
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q12.1) MUTATED     41   59
  DEL PEAK 13(5Q12.1) WILD-TYPE  166  173
        clus
vv       DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  FEMALE                          41                           166
  MALE                            59                           173
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q12.1) MUTATED    92   8
  DEL PEAK 13(5Q12.1) WILD-TYPE 286  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q12.1) MUTATED     92    8
  DEL PEAK 13(5Q12.1) WILD-TYPE  286   51
                               clus
vv                              DEL PEAK 13(5Q12.1) MUTATED
  COLON ADENOCARCINOMA                                   92
  COLON MUCINOUS ADENOCARCINOMA                           8
                               clus
vv                              DEL PEAK 13(5Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    286
  COLON MUCINOUS ADENOCARCINOMA                            51
[1] 2 2
[1] FALSE
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q12.1) MUTATED     3  97
  DEL PEAK 13(5Q12.1) WILD-TYPE   0 339
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q12.1) MUTATED      3   97
  DEL PEAK 13(5Q12.1) WILD-TYPE    0  339
     clus
vv    DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  NO                            3                             0
  YES                          97                           339
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q12.1) MUTATED    67   1   6   4
  DEL PEAK 13(5Q12.1) WILD-TYPE 246   2  18  21
D38V10, multiclass
    clus
vv   DEL PEAK 13(5Q12.1) MUTATED DEL PEAK 13(5Q12.1) WILD-TYPE
  R0                          67                           246
  R1                           1                             2
  R2                           6                            18
  RX                           4                            21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(5Q12.1) MUTATED                                  1     2
  DEL PEAK 13(5Q12.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(5Q12.1) MUTATED                          12    53
  DEL PEAK 13(5Q12.1) WILD-TYPE                        38   158
D38V12, multiclass
                                  clus
vv                                 DEL PEAK 13(5Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     53
                                  clus
vv                                 DEL PEAK 13(5Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = DEL PEAK 14(5Q21.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q21.1) MUTATED    88  31
  DEL PEAK 14(5Q21.1) WILD-TYPE 247  56
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                          119                           303 
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                           31                            56 
$`DEL PEAK 14(5Q21.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 
       37.02        43.76        13.94        15.52        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       14.53        30.44        29.19        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 
       25.18        24.16        21.76        23.87         9.63         5.03 
TCGA-AA-3496 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 
        1.02         1.02        37.05        19.07        26.01        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3673 
       13.02        24.00        23.01        19.99        61.02        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 
       47.01        15.02        11.01        19.00        85.05         0.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       36.95        37.02         0.99        33.07         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 
       31.07        17.03        24.03        24.00         2.01        21.99 
TCGA-AA-3994 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D 
       27.02        34.03        27.02        42.02        15.02         0.99 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6901 
       33.04         2.96         2.01         5.03        41.00         1.02 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4614 TCGA-AZ-4681 
        0.10         0.20        16.31         0.20         5.65        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5797 
       65.00        62.79        29.56         5.23         1.94         3.29 
TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 
        1.35        48.20         8.02        26.04         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 
       29.06        22.03         5.03        15.02        14.04        29.03 
TCGA-CM-6169 TCGA-CM-6675 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 
       13.02        13.05        19.59        20.42        15.12        17.85 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 
       10.13        12.43         9.04        13.41        11.38        92.75 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      140.38        44.32         7.76         6.12        14.04        26.47 
TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6808 
      117.07        98.24         8.61        13.38         1.55        33.67 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6625 TCGA-NH-A50T 
        8.35        82.39        45.11        36.00        91.79         4.11 
TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-RU-A8FL 
       10.98         1.32        26.99         6.64        30.28 

$`DEL PEAK 14(5Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        45.60        37.05        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       34.65        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        29.16        22.52         8.38 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        52.44         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
        1.02        37.05        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
        1.02        13.02        38.99         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 
        8.05        19.07        34.03        29.00        29.00         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        13.94        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3681 TCGA-AA-3685 
        2.01        14.01         0.92        47.05         5.98        37.05 
TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       36.00         5.03        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 
       14.93        17.03        36.03        32.05        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        18.05        18.05        17.03         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F 
       17.03        14.99        21.99        34.98        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       39.98         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        1.58         0.76         0.43         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        15.75        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94         5.13        22.36        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10       100.01        11.74         3.19         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
        2.14         3.25         0.07         0.26         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       102.44        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       20.02        37.02        27.02        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       12.95        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 
       14.99        12.26        13.51        11.51        20.19        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25         1.32         7.92         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 
       16.14        15.58         7.53        12.39        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
       38.20       130.65        49.91        13.32        12.59         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      131.51       135.65       139.17        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       60.79        95.18        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
       35.87        16.31        29.59        16.24         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 
       35.41        19.43       107.67        28.21        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       39.42        35.93        36.72        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       13.78        35.80        26.17        46.75        47.15        52.80 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.52         2.79         5.98         5.59         5.19         5.49 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 
       17.29        14.76        67.00 

  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE 
                        19.07                         19.99 
[1] "0.1 - 140.4 (19.1)" "0.1 - 139.2 (20.0)"
[1] "hr=" "1.5"
D39V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 14(5Q21.1) MUTATED        16        0        5        25         0
  DEL PEAK 14(5Q21.1) WILD-TYPE      56        1       23       106         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q21.1) MUTATED           0         4          8         17
  DEL PEAK 14(5Q21.1) WILD-TYPE         1        17          4         38
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 14(5Q21.1) MUTATED           16       16         8         2
  DEL PEAK 14(5Q21.1) WILD-TYPE         22       27        10         0
D39V3, multiclass
            clus
vv           DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  STAGE I                             16                            56
  STAGE IA                             0                             1
  STAGE II                             5                            23
  STAGE IIA                           25                           106
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            4                            17
  STAGE IIIA                           8                             4
  STAGE IIIB                          17                            38
  STAGE IIIC                          16                            22
  STAGE IV                            16                            27
  STAGE IVA                            8                            10
  STAGE IVB                            2                             0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 14(5Q21.1) MUTATED     3  20  83  15
  DEL PEAK 14(5Q21.1) WILD-TYPE   8  56 217  36
D39V4, multiclass
    clus
vv   DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  T1                           3                             8
  T2                          20                            56
  T3                          83                           217
  T4                          15                            36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 14(5Q21.1) MUTATED    53  37  31
  DEL PEAK 14(5Q21.1) WILD-TYPE 203  66  48
D39V5, multiclass
    clus
vv   DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  N0                          53                           203
  N1                          37                            66
  N2                          31                            48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 14(5Q21.1) MUTATED    79  18   6   2  15
  DEL PEAK 14(5Q21.1) WILD-TYPE 241  34   2   0  35
D39V6, multiclass
     clus
vv    DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  M0                           79                           241
  M1                           18                            34
  M1A                           6                             2
  M1B                           2                             0
  MX                           15                            35
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q21.1) MUTATED    51  70
  DEL PEAK 14(5Q21.1) WILD-TYPE 156 162
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q21.1) MUTATED     51   70
  DEL PEAK 14(5Q21.1) WILD-TYPE  156  162
        clus
vv       DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  FEMALE                          51                           156
  MALE                            70                           162
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q21.1) MUTATED   107  13
  DEL PEAK 14(5Q21.1) WILD-TYPE 271  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q21.1) MUTATED    107   13
  DEL PEAK 14(5Q21.1) WILD-TYPE  271   46
                               clus
vv                              DEL PEAK 14(5Q21.1) MUTATED
  COLON ADENOCARCINOMA                                  107
  COLON MUCINOUS ADENOCARCINOMA                          13
                               clus
vv                              DEL PEAK 14(5Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    271
  COLON MUCINOUS ADENOCARCINOMA                            46
[1] 2 2
[1] FALSE
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q21.1) MUTATED     3 118
  DEL PEAK 14(5Q21.1) WILD-TYPE   0 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q21.1) MUTATED      3  118
  DEL PEAK 14(5Q21.1) WILD-TYPE    0  318
     clus
vv    DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  NO                            3                             0
  YES                         118                           318
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q21.1) MUTATED    78   1   9   5
  DEL PEAK 14(5Q21.1) WILD-TYPE 235   2  15  20
D39V10, multiclass
    clus
vv   DEL PEAK 14(5Q21.1) MUTATED DEL PEAK 14(5Q21.1) WILD-TYPE
  R0                          78                           235
  R1                           1                             2
  R2                           9                            15
  RX                           5                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(5Q21.1) MUTATED                                  1     2
  DEL PEAK 14(5Q21.1) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q21.1) MUTATED                          12    63
  DEL PEAK 14(5Q21.1) WILD-TYPE                        38   148
D39V12, multiclass
                                  clus
vv                                 DEL PEAK 14(5Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     63
                                  clus
vv                                 DEL PEAK 14(5Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      148
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = DEL PEAK 15(5Q22.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(5Q22.2) MUTATED    88  32
  DEL PEAK 15(5Q22.2) WILD-TYPE 247  55
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                          120                           302 
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                           32                            55 
$`DEL PEAK 15(5Q22.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 
       37.02        43.76        13.94        15.52        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       14.53        30.44        29.19        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 
       25.18        24.16        21.76        23.87         9.63         5.03 
TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3538 TCGA-AA-3542 
        1.02         1.02        37.05        19.07        26.01        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3673 TCGA-AA-3678 
       13.02        24.00        19.99        61.02        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3841 
       15.02        19.00        85.05        19.04         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       37.02         0.99        33.07         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3986 TCGA-AA-A00F 
       24.03        24.00         2.01        21.99        19.07        34.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02E 
       27.02        42.02        15.02         0.99        33.04         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
        2.01         5.03        41.00         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4614 TCGA-AZ-4681 
        0.20        16.31         0.20        21.44         5.65        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 
       65.00        62.79         6.77        29.56         5.23         1.94 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-6751 TCGA-CM-4747 
        2.14         3.29         1.35        48.20       124.27         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
       26.04         8.02        13.02        22.03         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6677 TCGA-D5-5539 TCGA-D5-6535 
       14.04        29.03        13.02        11.08        19.59        15.12 
TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       17.85        10.13        12.43         9.04        13.41        11.38 
TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A28A 
       92.75       140.38        44.32         7.76         6.12        26.47 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 
       60.79       117.07        98.24         8.61        13.38         1.55 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6317 TCGA-G4-6625 
       33.67         8.35        82.39        45.11        36.00        91.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-RU-A8FL 
        4.11        10.98         1.32        26.99         6.64        30.28 

$`DEL PEAK 15(5Q22.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        45.60        37.05        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       34.65        32.45        32.91        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 
       22.09        22.06        32.71        29.16        22.52         8.38 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        61.84        52.44         1.02         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
       37.05        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       13.02        38.99         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 
        8.05        19.07        34.03        29.00        29.00         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        33.99        21.01        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        13.94        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 
       54.02         2.01        14.01         0.92        47.05        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 
        5.98        37.05        36.00         5.03        26.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 
       38.99        14.93        17.03        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       25.02        24.00        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       38.04        19.00        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
        4.01         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.06        51.98        39.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.79         0.72         1.58         0.43         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L 
       14.50        27.09         0.95        15.75        17.82         5.19 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       32.94         5.13        22.36        61.41        49.41        12.10 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
      100.01        11.74         3.19         2.24         3.06         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        0.07         0.26         0.33         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 
        2.93         2.01        23.05        20.02        37.02        27.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       29.06        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        15.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        14.99        12.26 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        1.32         7.92         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58         7.53        12.39        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        49.91        13.32        12.59         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       95.18        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       16.31        29.59        16.24         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       19.43       107.67        28.21        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        51.75        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       35.80        26.17        46.75        47.15        52.80        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX 
        2.79         5.98         5.59         5.19         5.49        17.29 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       14.76        67.00 

  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE 
                       19.020                        20.155 
[1] "0.1 - 140.4 (19.0)" "0.1 - 139.2 (20.2)"
[1] "hr=" "1.5"
D40V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 15(5Q22.2) MUTATED        17        0        6        28         0
  DEL PEAK 15(5Q22.2) WILD-TYPE      55        1       22       103         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(5Q22.2) MUTATED           0         5          7         15
  DEL PEAK 15(5Q22.2) WILD-TYPE         1        16          5         40
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 15(5Q22.2) MUTATED           15       18         8         1
  DEL PEAK 15(5Q22.2) WILD-TYPE         23       25        10         1
D40V3, multiclass
            clus
vv           DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  STAGE I                             17                            55
  STAGE IA                             0                             1
  STAGE II                             6                            22
  STAGE IIA                           28                           103
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            5                            16
  STAGE IIIA                           7                             5
  STAGE IIIB                          15                            40
  STAGE IIIC                          15                            23
  STAGE IV                            18                            25
  STAGE IVA                            8                            10
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 15(5Q22.2) MUTATED     3  20  87  15
  DEL PEAK 15(5Q22.2) WILD-TYPE   8  56 213  36
D40V4, multiclass
    clus
vv   DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  T1                           3                             8
  T2                          20                            56
  T3                          87                           213
  T4                          15                            36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 15(5Q22.2) MUTATED    60  34  31
  DEL PEAK 15(5Q22.2) WILD-TYPE 196  69  48
D40V5, multiclass
    clus
vv   DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  N0                          60                           196
  N1                          34                            69
  N2                          31                            48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 15(5Q22.2) MUTATED    78  20   6   1  17
  DEL PEAK 15(5Q22.2) WILD-TYPE 242  32   2   1  33
D40V6, multiclass
     clus
vv    DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  M0                           78                           242
  M1                           20                            32
  M1A                           6                             2
  M1B                           1                             1
  MX                           17                            33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q22.2) MUTATED    51  74
  DEL PEAK 15(5Q22.2) WILD-TYPE 156 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q22.2) MUTATED     51   74
  DEL PEAK 15(5Q22.2) WILD-TYPE  156  158
        clus
vv       DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  FEMALE                          51                           156
  MALE                            74                           158
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q22.2) MUTATED   113  12
  DEL PEAK 15(5Q22.2) WILD-TYPE 265  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q22.2) MUTATED    113   12
  DEL PEAK 15(5Q22.2) WILD-TYPE  265   47
                               clus
vv                              DEL PEAK 15(5Q22.2) MUTATED
  COLON ADENOCARCINOMA                                  113
  COLON MUCINOUS ADENOCARCINOMA                          12
                               clus
vv                              DEL PEAK 15(5Q22.2) WILD-TYPE
  COLON ADENOCARCINOMA                                    265
  COLON MUCINOUS ADENOCARCINOMA                            47
[1] 2 2
[1] FALSE
D40V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q22.2) MUTATED     3 122
  DEL PEAK 15(5Q22.2) WILD-TYPE   0 314
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q22.2) MUTATED      3  122
  DEL PEAK 15(5Q22.2) WILD-TYPE    0  314
     clus
vv    DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  NO                            3                             0
  YES                         122                           314
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(5Q22.2) MUTATED    77   1  11   6
  DEL PEAK 15(5Q22.2) WILD-TYPE 236   2  13  19
D40V10, multiclass
    clus
vv   DEL PEAK 15(5Q22.2) MUTATED DEL PEAK 15(5Q22.2) WILD-TYPE
  R0                          77                           236
  R1                           1                             2
  R2                          11                            13
  RX                           6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(5Q22.2) MUTATED                                  1     3
  DEL PEAK 15(5Q22.2) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(5Q22.2) MUTATED                          11    66
  DEL PEAK 15(5Q22.2) WILD-TYPE                        39   145
D40V12, multiclass
                                  clus
vv                                 DEL PEAK 15(5Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     66
                                  clus
vv                                 DEL PEAK 15(5Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   39
  WHITE                                                      145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = DEL PEAK 16(6P25.3) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(6P25.3) MUTATED    39  14
  DEL PEAK 16(6P25.3) WILD-TYPE 296  73
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           53                           369 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           14                            73 
$`DEL PEAK 16(6P25.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6782 
       37.02        15.52        16.04        25.18        24.16        20.28 
TCGA-AA-3518 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3685 
        1.02        13.94        61.02         6.97         2.01        37.05 
TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3858 TCGA-AA-3864 
       36.00         0.99        38.99        36.95        31.07        53.00 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A004 
       29.98        18.05        12.99        24.00         2.01        13.94 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02O 
       30.02        18.05        27.02        38.07        26.01         0.92 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AZ-4614 TCGA-AZ-6607 
        0.72         1.58         0.76         0.43         5.65         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-6676 
        2.24         3.06         2.14        29.06        22.98        11.08 
TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6898 
       11.01        14.99        20.19        17.75        17.85         7.53 
TCGA-DM-A1D7 TCGA-DM-A28A TCGA-DM-A28H TCGA-F4-6808 TCGA-G4-6317 
       13.32        26.47       117.07        33.67        36.00 

$`DEL PEAK 16(6P25.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       22.09        22.06        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        52.44         9.63         5.03         1.02         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        1.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
        6.97         1.02        13.02        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       23.01        20.98        19.99        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       15.02        11.01         5.98        19.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       26.99        19.04         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        15.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       17.03        24.03        27.02        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       26.01        24.00         2.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A 
       24.00        27.02        19.07         7.96        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q 
       19.00        34.03        18.05        17.03         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
       22.03        41.00        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 
       21.37         4.21        56.55         0.79         1.02         0.10 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.20         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.95        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.52         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        5.23        11.74         1.94         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        0.26         0.33         0.10         1.35        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       37.02         8.02        26.04         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        30.08        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       16.04        21.99        14.99        12.99        13.02        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.08        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       12.03        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       18.25         1.32         7.92        15.12         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K 
       14.04        81.37       119.93        35.97        60.79        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       14.76        30.28        67.00 

  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                       117.07                        140.38 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                        17.85                         19.99 
[1] "0.4 - 117.1 (17.9)" "0.1 - 140.4 (20.0)"
[1] "hr=" "1.7"
D41V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 16(6P25.3) MUTATED         7        0        6        17         1
  DEL PEAK 16(6P25.3) WILD-TYPE      65        1       22       114         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6P25.3) MUTATED           0         3          1          3
  DEL PEAK 16(6P25.3) WILD-TYPE         1        18         11         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 16(6P25.3) MUTATED            5        5         4         0
  DEL PEAK 16(6P25.3) WILD-TYPE         33       38        14         2
D41V3, multiclass
            clus
vv           DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  STAGE I                              7                            65
  STAGE IA                             0                             1
  STAGE II                             6                            22
  STAGE IIA                           17                           114
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           1                            11
  STAGE IIIB                           3                            52
  STAGE IIIC                           5                            33
  STAGE IV                             5                            38
  STAGE IVA                            4                            14
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 16(6P25.3) MUTATED     2   7  36   9
  DEL PEAK 16(6P25.3) WILD-TYPE   9  69 264  42
D41V4, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  T1                           2                             9
  T2                           7                            69
  T3                          36                           264
  T4                           9                            42
[1] 4 2
[1] 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
  DEL PEAK 16(6P25.3) MUTATED    33  11  10
  DEL PEAK 16(6P25.3) WILD-TYPE 223  92  69
D41V5, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  N0                          33                           223
  N1                          11                            92
  N2                          10                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 16(6P25.3) MUTATED    37   6   3   0   7
  DEL PEAK 16(6P25.3) WILD-TYPE 283  46   5   2  43
D41V6, multiclass
     clus
vv    DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  M0                           37                           283
  M1                            6                            46
  M1A                           3                             5
  M1B                           0                             2
  MX                            7                            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"
D41V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    19  35
  DEL PEAK 16(6P25.3) WILD-TYPE 188 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     19   35
  DEL PEAK 16(6P25.3) WILD-TYPE  188  197
        clus
vv       DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  FEMALE                          19                           188
  MALE                            35                           197
[1] 2 2
[1] FALSE
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    49   5
  DEL PEAK 16(6P25.3) WILD-TYPE 329  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     49    5
  DEL PEAK 16(6P25.3) WILD-TYPE  329   54
                               clus
vv                              DEL PEAK 16(6P25.3) MUTATED
  COLON ADENOCARCINOMA                                   49
  COLON MUCINOUS ADENOCARCINOMA                           5
                               clus
vv                              DEL PEAK 16(6P25.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    329
  COLON MUCINOUS ADENOCARCINOMA                            54
[1] 2 2
[1] FALSE
D41V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED     0  54
  DEL PEAK 16(6P25.3) WILD-TYPE   3 382
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED      0   54
  DEL PEAK 16(6P25.3) WILD-TYPE    3  382
     clus
vv    DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  NO                            0                             3
  YES                          54                           382
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(6P25.3) MUTATED    37   0   1   5
  DEL PEAK 16(6P25.3) WILD-TYPE 276   3  23  20
D41V10, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  R0                          37                           276
  R1                           0                             3
  R2                           1                            23
  RX                           5                            20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(6P25.3) MUTATED                                  0     3
  DEL PEAK 16(6P25.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6P25.3) MUTATED                           1    26
  DEL PEAK 16(6P25.3) WILD-TYPE                        49   185
D41V12, multiclass
                                  clus
vv                                 DEL PEAK 16(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     26
                                  clus
vv                                 DEL PEAK 16(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   49
  WHITE                                                      185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = DEL PEAK 17(6Q26) MUTATION ANALYSIS
D42V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 17(6Q26) MUTATED    41  18
  DEL PEAK 17(6Q26) WILD-TYPE 294  69
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         59                         363 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         18                          69 
$`DEL PEAK 17(6Q26) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-4107 TCGA-A6-6138 TCGA-A6-6649 
       37.02        42.28        45.60        32.45        22.52        24.16 
TCGA-A6-6782 TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 
       20.28         5.03        13.02        61.02        54.02         2.01 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3837 
       11.01        37.05        36.00        85.05         0.99        38.99 
TCGA-AA-3841 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       36.95        36.03        31.07        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-A00J TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X 
        2.01        18.05        17.03         0.99        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 
        2.96         2.01         1.58         0.43         0.46        16.31 
TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 
        0.20         6.87         5.13        49.41         3.19         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
        3.06         2.14        11.01        13.05        11.08        11.01 
TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-DM-A1D7 
       14.99        20.19        17.75        15.12         7.53        13.32 
TCGA-DM-A1HA TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6297 TCGA-NH-A6GA 
      131.51         1.55        33.67        82.39         5.98 

$`DEL PEAK 17(6Q26) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       17.79        44.91        35.11        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.25        16.04        34.65        36.53        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       52.44         9.63         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        19.99        78.08         6.05         6.97 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       14.01         0.92        50.04        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 
        5.98        19.00         5.03        26.99        19.04         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        53.00        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       29.98        31.00         2.01        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       51.98        39.98         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 
       56.55         0.79         0.72         1.02         0.10         0.76 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.20         0.92        14.50        27.09         0.95        15.75 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 
       21.44        17.82         5.19         5.52        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       65.00        62.79        61.41         6.77        12.10       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-5797 
       29.56         5.23        11.74         1.94         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       20.02        37.02         8.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 
       12.99        13.02        15.02        14.04        12.95        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.42        18.25         1.32         7.92        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
        1.51        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       16.24         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       28.21         8.35        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       35.93        36.72        36.00        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       13.78        35.80        26.17        91.79        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       52.80         4.11        10.98        10.52         2.79         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       14.76        30.28        67.00 

  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                       0.20                        0.07 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                     131.51                      140.38 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                      15.12                       20.42 
[1] "0.2 - 131.5 (15.1)" "0.1 - 140.4 (20.4)"
[1] "hr=" "1.9"
D42V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 17(6Q26) MUTATED         8        0        6        11         1
  DEL PEAK 17(6Q26) WILD-TYPE      64        1       22       120         7
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q26) MUTATED           0         4          0          8
  DEL PEAK 17(6Q26) WILD-TYPE         1        17         12         47
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 17(6Q26) MUTATED            9        9         4         1
  DEL PEAK 17(6Q26) WILD-TYPE         29       34        14         1
D42V3, multiclass
            clus
vv           DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  STAGE I                            8                          64
  STAGE IA                           0                           1
  STAGE II                           6                          22
  STAGE IIA                         11                         120
  STAGE IIB                          1                           7
  STAGE IIC                          0                           1
  STAGE III                          4                          17
  STAGE IIIA                         0                          12
  STAGE IIIB                         8                          47
  STAGE IIIC                         9                          29
  STAGE IV                           9                          34
  STAGE IVA                          4                          14
  STAGE IVB                          1                           1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 17(6Q26) MUTATED     2   7  43   9
  DEL PEAK 17(6Q26) WILD-TYPE   9  69 257  42
D42V4, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  T1                         2                           9
  T2                         7                          69
  T3                        43                         257
  T4                         9                          42
[1] 4 2
[1] 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
  DEL PEAK 17(6Q26) MUTATED    27  14  20
  DEL PEAK 17(6Q26) WILD-TYPE 229  89  59
D42V5, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  N0                        27                         229
  N1                        14                          89
  N2                        20                          59
[1] 3 2
[1] 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 M1A M1B  MX
  DEL PEAK 17(6Q26) MUTATED    37  11   2   1   9
  DEL PEAK 17(6Q26) WILD-TYPE 283  41   6   1  41
D42V6, multiclass
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  M0                         37                         283
  M1                         11                          41
  M1A                         2                           6
  M1B                         1                           1
  MX                          9                          41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    27  34
  DEL PEAK 17(6Q26) WILD-TYPE 180 198
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     27   34
  DEL PEAK 17(6Q26) WILD-TYPE  180  198
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  FEMALE                        27                         180
  MALE                          34                         198
[1] 2 2
[1] FALSE
D42V8, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    53   8
  DEL PEAK 17(6Q26) WILD-TYPE 325  51
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     53    8
  DEL PEAK 17(6Q26) WILD-TYPE  325   51
                               clus
vv                              DEL PEAK 17(6Q26) MUTATED
  COLON ADENOCARCINOMA                                 53
  COLON MUCINOUS ADENOCARCINOMA                         8
                               clus
vv                              DEL PEAK 17(6Q26) WILD-TYPE
  COLON ADENOCARCINOMA                                  325
  COLON MUCINOUS ADENOCARCINOMA                          51
[1] 2 2
[1] FALSE
D42V9, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED     0  61
  DEL PEAK 17(6Q26) WILD-TYPE   3 375
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      0   61
  DEL PEAK 17(6Q26) WILD-TYPE    3  375
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  NO                          0                           3
  YES                        61                         375
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 17(6Q26) MUTATED    40   1   5   6
  DEL PEAK 17(6Q26) WILD-TYPE 273   2  19  19
D42V10, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  R0                        40                         273
  R1                         1                           2
  R2                         5                          19
  RX                         6                          19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(6Q26) MUTATED                                  1     3
  DEL PEAK 17(6Q26) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(6Q26) MUTATED                           5    26
  DEL PEAK 17(6Q26) WILD-TYPE                        45   185
D42V12, multiclass
                                  clus
vv                                 DEL PEAK 17(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   26
                                  clus
vv                                 DEL PEAK 17(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 45
  WHITE                                                    185
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = DEL PEAK 18(7Q31.1) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(7Q31.1) MUTATED     9   2
  DEL PEAK 18(7Q31.1) WILD-TYPE 326  85
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           11                           411 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                            2                            85 
$`DEL PEAK 18(7Q31.1) MUTATED`
TCGA-A6-3807 TCGA-AA-A00L TCGA-AA-A01R TCGA-AD-6548 TCGA-AU-3779 TCGA-CM-5341 
       34.65        17.03        35.01        21.37        14.50        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6170 TCGA-D5-6932 TCGA-DM-A0XD 
       22.03         5.03        15.02        11.38        24.43 

$`DEL PEAK 18(7Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       13.94        15.52        37.05        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.16        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
        1.02        13.02        38.99         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       33.99        21.01        13.02        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
        5.98        37.05        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02         0.99        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07         1.02         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       26.01        37.02        39.06        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
        2.01         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05        40.96         0.07         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         1.58         1.02         0.10         0.76         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.43         0.46         0.92        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
        5.23        11.74         3.19         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        2.14         3.25         3.29         0.07         0.26         0.33 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.10         1.35        17.56       102.44        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.01       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
       26.04         8.02        27.02        13.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       16.01        15.02        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       12.99        13.02        14.04        11.01        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.08        11.08        11.01        10.06        12.03        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       12.26        19.59        13.51        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25         1.32         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.41         1.51        12.00        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        1.32         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
       14.76        30.28        67.00 

  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                         5.03                          0.07 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        35.01                        140.38 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        21.37                         19.59 
[1] "5.0 - 35.0 (21.4)"  "0.1 - 140.4 (19.6)"
[1] "hr=" "1.1"
D43V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 18(7Q31.1) MUTATED         2        0        0         5         0
  DEL PEAK 18(7Q31.1) WILD-TYPE      70        1       28       126         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(7Q31.1) MUTATED           0         1          1          1
  DEL PEAK 18(7Q31.1) WILD-TYPE         1        20         11         54
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 18(7Q31.1) MUTATED            1        0         1         0
  DEL PEAK 18(7Q31.1) WILD-TYPE         37       43        17         2
D43V3, multiclass
            clus
vv           DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  STAGE I                              2                            70
  STAGE IA                             0                             1
  STAGE II                             0                            28
  STAGE IIA                            5                           126
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            1                            20
  STAGE IIIA                           1                            11
  STAGE IIIB                           1                            54
  STAGE IIIC                           1                            37
  STAGE IV                             0                            43
  STAGE IVA                            1                            17
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 18(7Q31.1) MUTATED     0   3   9   0
  DEL PEAK 18(7Q31.1) WILD-TYPE  11  73 291  51
D43V4, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  T1                           0                            11
  T2                           3                            73
  T3                           9                           291
  T4                           0                            51
[1] 4 2
[1] 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
  DEL PEAK 18(7Q31.1) MUTATED     7   3   2
  DEL PEAK 18(7Q31.1) WILD-TYPE 249 100  77
D43V5, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  N0                           7                           249
  N1                           3                           100
  N2                           2                            77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 18(7Q31.1) MUTATED    11   0   1   0   0
  DEL PEAK 18(7Q31.1) WILD-TYPE 309  52   7   2  50
D43V6, multiclass
     clus
vv    DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  M0                           11                           309
  M1                            0                            52
  M1A                           1                             7
  M1B                           0                             2
  MX                            0                            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"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED     7   5
  DEL PEAK 18(7Q31.1) WILD-TYPE 200 227
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      7    5
  DEL PEAK 18(7Q31.1) WILD-TYPE  200  227
        clus
vv       DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  FEMALE                           7                           200
  MALE                             5                           227
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED    11   1
  DEL PEAK 18(7Q31.1) WILD-TYPE 367  58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     11    1
  DEL PEAK 18(7Q31.1) WILD-TYPE  367   58
                               clus
vv                              DEL PEAK 18(7Q31.1) MUTATED
  COLON ADENOCARCINOMA                                   11
  COLON MUCINOUS ADENOCARCINOMA                           1
                               clus
vv                              DEL PEAK 18(7Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    367
  COLON MUCINOUS ADENOCARCINOMA                            58
[1] 2 2
[1] FALSE
D43V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED     0  12
  DEL PEAK 18(7Q31.1) WILD-TYPE   3 424
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      0   12
  DEL PEAK 18(7Q31.1) WILD-TYPE    3  424
     clus
vv    DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  NO                            0                             3
  YES                          12                           424
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(7Q31.1) MUTATED    11   0   0   0
  DEL PEAK 18(7Q31.1) WILD-TYPE 302   3  24  25
D43V10, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  R0                          11                           302
  R1                           0                             3
  R2                           0                            24
  RX                           0                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(7Q31.1) MUTATED                                  0     0
  DEL PEAK 18(7Q31.1) WILD-TYPE                                1    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(7Q31.1) MUTATED                           0     9
  DEL PEAK 18(7Q31.1) WILD-TYPE                        50   202
D43V12, multiclass
                                  clus
vv                                 DEL PEAK 18(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                      9
                                  clus
vv                                 DEL PEAK 18(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   50
  WHITE                                                      202
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = DEL PEAK 19(8P23.3) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(8P23.3) MUTATED   141  38
  DEL PEAK 19(8P23.3) WILD-TYPE 194  49
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                          179                           243 
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                           38                            49 
$`DEL PEAK 19(8P23.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       37.02        43.76        43.43        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       35.11        45.60        15.52        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       31.63        29.19        29.16        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       25.18        20.61        24.69        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
       52.44         9.63         5.03         1.02        37.05         1.02 
TCGA-AA-3506 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       58.03        38.99        24.03        34.03        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        14.01        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       23.01        19.99        19.99        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 
       14.01        47.01        15.02         5.98        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       36.00        85.05        37.02        33.07        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 
       31.07        31.07        17.03        24.03        27.02        29.98 
TCGA-AA-3930 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 
        2.01         2.01        34.03         2.01        16.08        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       26.01        24.00        27.02         7.96        19.00        34.03 
TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       17.03        15.02        12.00        31.00         1.02        33.04 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 
       37.02         2.96        39.98        41.00        40.96         4.21 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 
        1.58         1.02         0.20        16.31        15.75         0.20 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 
        5.52         6.87        75.25         5.65        83.80        65.00 
TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       62.79        12.10        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5912 
        1.94         3.29         0.07         1.35        15.62        48.20 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        22.03        22.98        30.08        16.01 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
        5.03        17.03        14.04        21.99        13.02        15.02 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5541 TCGA-D5-6531 
       13.05        11.08        10.06        12.26        11.51        17.75 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
        1.32         7.92        15.12        12.49        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD 
       10.13        12.43         9.04        13.41        11.38        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA 
       38.20       130.65        49.91        13.32       140.38       131.51 
TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 
        6.12        26.47        35.97        60.79       117.07        13.38 
TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 
       13.64         1.55        16.31         0.53         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       74.56        61.87        44.68        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A50U TCGA-NH-A50V 
       36.00        26.43        35.80        91.79        10.98        10.52 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-RU-A8FL 
        5.98         5.59         5.49         6.64        30.28 

$`DEL PEAK 19(8P23.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2684 
        5.06         5.26        46.65        23.38        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5661 
       37.25        16.04        14.53        32.45        30.44        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 
       23.61        22.09        22.06        32.71        22.52         8.38 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       24.16        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
       24.92         1.02         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02         1.02         9.07        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3548 TCGA-AA-3554 
        8.05        19.07        19.07        29.00        33.99        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        61.02         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 
        0.92        50.04        47.05        11.01         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        36.95        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 
       17.03         0.99        32.05        53.00        18.05        31.00 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       12.99        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       21.99        50.99        13.05        25.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       13.94        38.04        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02        42.02         0.99        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02         0.99        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        35.01        26.01        39.06        51.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
        2.01         5.03         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 
        0.07        21.37        56.55         0.79         0.72         0.10 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.76         0.43         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 
        0.95        21.44        17.82         5.19        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        32.94         5.13        22.36        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        6.77       100.01         2.24         3.06         2.14         3.25 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.26         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02         8.02        26.04 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
        8.02        29.06        15.02        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       12.00        29.03        16.04        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       11.01        12.95        11.08        11.01        12.03        14.99 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 
       19.59        13.51        20.19        20.42        18.25        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 
        4.50        17.13        16.14        12.39        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 
       11.64         1.51        12.00        10.26       119.70        92.75 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       14.04        81.37       119.93        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 
       11.11        13.45         6.18        35.87        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67         1.28        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       82.39        43.07        53.62        55.04        51.75        45.11 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       22.09        26.04        13.78        26.17        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV 
       52.80         4.11         2.79         1.32         5.19        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 
       17.29        14.76        67.00 

  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE 
                        20.61                         19.07 
[1] "0.1 - 140.4 (20.6)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1"  
D44V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 19(8P23.3) MUTATED        24        0        8        41         2
  DEL PEAK 19(8P23.3) WILD-TYPE      48        1       20        90         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(8P23.3) MUTATED           0        10          6         27
  DEL PEAK 19(8P23.3) WILD-TYPE         1        11          6         28
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 19(8P23.3) MUTATED           23       28        10         1
  DEL PEAK 19(8P23.3) WILD-TYPE         15       15         8         1
D44V3, multiclass
            clus
vv           DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  STAGE I                             24                            48
  STAGE IA                             0                             1
  STAGE II                             8                            20
  STAGE IIA                           41                            90
  STAGE IIB                            2                             6
  STAGE IIC                            0                             1
  STAGE III                           10                            11
  STAGE IIIA                           6                             6
  STAGE IIIB                          27                            28
  STAGE IIIC                          23                            15
  STAGE IV                            28                            15
  STAGE IVA                           10                             8
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 19(8P23.3) MUTATED     1  30 131  21
  DEL PEAK 19(8P23.3) WILD-TYPE  10  46 169  30
D44V4, multiclass
    clus
vv   DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  T1                           1                            10
  T2                          30                            46
  T3                         131                           169
  T4                          21                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 19(8P23.3) MUTATED    84  50  48
  DEL PEAK 19(8P23.3) WILD-TYPE 172  53  31
D44V5, multiclass
    clus
vv   DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  N0                          84                           172
  N1                          50                            53
  N2                          48                            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                             M0  M1 M1A M1B  MX
  DEL PEAK 19(8P23.3) MUTATED   123  33   5   1  19
  DEL PEAK 19(8P23.3) WILD-TYPE 197  19   3   1  31
D44V6, multiclass
     clus
vv    DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  M0                          123                           197
  M1                           33                            19
  M1A                           5                             3
  M1B                           1                             1
  MX                           19                            31
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.3) MUTATED    74 109
  DEL PEAK 19(8P23.3) WILD-TYPE 133 123
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.3) MUTATED     74  109
  DEL PEAK 19(8P23.3) WILD-TYPE  133  123
        clus
vv       DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  FEMALE                          74                           133
  MALE                           109                           123
[1] 2 2
[1] FALSE
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.3) MUTATED   165  17
  DEL PEAK 19(8P23.3) WILD-TYPE 213  42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.3) MUTATED    165   17
  DEL PEAK 19(8P23.3) WILD-TYPE  213   42
                               clus
vv                              DEL PEAK 19(8P23.3) MUTATED
  COLON ADENOCARCINOMA                                  165
  COLON MUCINOUS ADENOCARCINOMA                          17
                               clus
vv                              DEL PEAK 19(8P23.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    213
  COLON MUCINOUS ADENOCARCINOMA                            42
[1] 2 2
[1] FALSE
D44V9, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.3) MUTATED     2 181
  DEL PEAK 19(8P23.3) WILD-TYPE   1 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.3) MUTATED      2  181
  DEL PEAK 19(8P23.3) WILD-TYPE    1  255
     clus
vv    DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  NO                            2                             1
  YES                         181                           255
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 19(8P23.3) MUTATED   125   1  14   6
  DEL PEAK 19(8P23.3) WILD-TYPE 188   2  10  19
D44V10, multiclass
    clus
vv   DEL PEAK 19(8P23.3) MUTATED DEL PEAK 19(8P23.3) WILD-TYPE
  R0                         125                           188
  R1                           1                             2
  R2                          14                            10
  RX                           6                            19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(8P23.3) MUTATED                                  1     3
  DEL PEAK 19(8P23.3) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(8P23.3) MUTATED                          24    88
  DEL PEAK 19(8P23.3) WILD-TYPE                        26   123
D44V12, multiclass
                                  clus
vv                                 DEL PEAK 19(8P23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 24
  WHITE                                                     88
                                  clus
vv                                 DEL PEAK 19(8P23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   26
  WHITE                                                      123
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 20(8P22) MUTATION ANALYSIS
D45V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 20(8P22) MUTATED   147  46
  DEL PEAK 20(8P22) WILD-TYPE 188  41
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        193                         229 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                         46                          41 
$`DEL PEAK 20(8P22) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 
       37.02        43.76        43.43        17.79        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       35.11        45.60        15.52        34.65        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6137 
       31.63        30.44        29.19        23.61        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        25.18        20.61        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 
       20.28        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3532 
       37.05         1.02        38.99        24.03        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       24.00        23.01        19.99        19.99        78.08         6.05 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       54.02         2.01        14.01        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 
        5.98        37.05        19.00        36.00        85.05        37.02 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.99        33.07        36.03         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3956 
       17.03        24.03        27.02        29.98         2.01        34.03 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 
       16.08        34.06        26.01        24.00        27.02         7.96 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01G 
       19.00        34.03        17.03        17.03        15.02        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02J 
       31.00         1.02        33.04        37.02         2.96         5.03 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 
       41.00        40.96         4.21         1.58         1.02         0.20 
TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK 
        0.46        16.31        15.75         0.20         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       75.25         5.65        83.80        22.36        65.00        62.79 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
       12.10        29.56         5.23        11.74         3.19         1.94 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        3.29         0.07         1.35       102.44        15.62        48.20 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        22.03        22.98        30.08        16.01 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
        5.03        17.03        14.04        21.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        13.05        11.08        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 
       11.51        17.75         1.32         7.92        15.12        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 
       15.58         7.53        10.13        12.43         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 
       11.38        24.43        38.20       130.65        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28F 
      140.38        44.32       131.51         6.12        26.47        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07         8.61        13.38        11.11        13.64 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 
        1.55        16.31         1.28         0.53         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       74.56        61.87        44.68        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 
       36.00        26.43        26.04        35.80        91.79        46.75 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 
       10.98        10.52         5.98         5.59         5.49         6.64 
TCGA-RU-A8FL 
       30.28 

$`DEL PEAK 20(8P22) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2684 
        5.06         5.26        46.65        23.38        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5661 TCGA-A6-5664 
       37.25        16.04        14.53        32.45        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 
       22.06        32.71        22.52         8.38        24.16        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 
       24.39        20.12        19.66        16.24        24.92         1.02 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        3.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       13.02         1.02         9.07        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
       19.07        19.07        29.00         0.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 
       20.98        13.94        61.02         6.97         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       47.05         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3855 TCGA-AA-3864 
       38.99        36.95        14.93        17.03        32.05        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
       24.00         2.01        20.98         2.01        21.99        50.99 
TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       13.05        25.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D 
        0.99        14.99        21.99        34.98        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       32.02        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O 
       26.01        39.06        51.98        39.98         2.01         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 
       22.03        39.98        18.05         0.07        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5821 
        0.79         0.72         0.10         0.76         0.43         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       14.50        27.09         0.95        21.44        17.82         5.19 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5407 
       50.37        58.39         1.41        32.94         5.13        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       49.41         6.77       100.01         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 
        3.25         0.26         0.33         0.10        17.56        40.34 
TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02         8.02        26.04 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
        8.02        29.06        15.02        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       12.00        29.03        16.04        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        11.08        11.01        10.06        12.03        14.99 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.19        20.42        18.25        17.85         4.50        17.13 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       16.14        12.39        14.30         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA 
       12.00        10.26       119.70        92.75        12.59         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        14.04        81.37       119.93 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 
       98.24        95.18        13.45         6.18        35.87        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       16.24        33.67        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       82.39        43.07        53.62        55.04        51.75        45.11 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       22.09        13.78        26.17        47.15        52.80         4.11 
TCGA-NH-A5IV TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         1.32         5.19        26.99        17.29        14.76 
TCGA-WS-AB45 
       67.00 

  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                     140.38                      139.17 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                      20.61                       19.07 
[1] "0.1 - 140.4 (20.6)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1.3"
D45V2, continuous
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 20(8P22) MUTATED        23        0        9        42         2
  DEL PEAK 20(8P22) WILD-TYPE      49        1       19        89         6
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8P22) MUTATED           0        10          8         30
  DEL PEAK 20(8P22) WILD-TYPE         1        11          4         25
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 20(8P22) MUTATED           25       29        14         1
  DEL PEAK 20(8P22) WILD-TYPE         13       14         4         1
D45V3, multiclass
            clus
vv           DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  STAGE I                           23                          49
  STAGE IA                           0                           1
  STAGE II                           9                          19
  STAGE IIA                         42                          89
  STAGE IIB                          2                           6
  STAGE IIC                          0                           1
  STAGE III                         10                          11
  STAGE IIIA                         8                           4
  STAGE IIIB                        30                          25
  STAGE IIIC                        25                          13
  STAGE IV                          29                          14
  STAGE IVA                         14                           4
  STAGE IVB                          1                           1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 20(8P22) MUTATED     1  29 142  24
  DEL PEAK 20(8P22) WILD-TYPE  10  47 158  27
D45V4, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  T1                         1                          10
  T2                        29                          47
  T3                       142                         158
  T4                        24                          27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           N0  N1  N2
  DEL PEAK 20(8P22) MUTATED    87  54  54
  DEL PEAK 20(8P22) WILD-TYPE 169  49  25
D45V5, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  N0                        87                         169
  N1                        54                          49
  N2                        54                          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                           M0  M1 M1A M1B  MX
  DEL PEAK 20(8P22) MUTATED   130  38   5   1  20
  DEL PEAK 20(8P22) WILD-TYPE 190  14   3   1  30
D45V6, multiclass
     clus
vv    DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  M0                        130                         190
  M1                         38                          14
  M1A                         5                           3
  M1B                         1                           1
  MX                         20                          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"
D45V7, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED    82 114
  DEL PEAK 20(8P22) WILD-TYPE 125 118
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED     82  114
  DEL PEAK 20(8P22) WILD-TYPE  125  118
        clus
vv       DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  FEMALE                        82                         125
  MALE                         114                         118
[1] 2 2
[1] FALSE
D45V8, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED   178  17
  DEL PEAK 20(8P22) WILD-TYPE 200  42
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED    178   17
  DEL PEAK 20(8P22) WILD-TYPE  200   42
                               clus
vv                              DEL PEAK 20(8P22) MUTATED
  COLON ADENOCARCINOMA                                178
  COLON MUCINOUS ADENOCARCINOMA                        17
                               clus
vv                              DEL PEAK 20(8P22) WILD-TYPE
  COLON ADENOCARCINOMA                                  200
  COLON MUCINOUS ADENOCARCINOMA                          42
[1] 2 2
[1] FALSE
D45V9, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED     2 194
  DEL PEAK 20(8P22) WILD-TYPE   1 242
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED      2  194
  DEL PEAK 20(8P22) WILD-TYPE    1  242
     clus
vv    DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  NO                          2                           1
  YES                       194                         242
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 20(8P22) MUTATED   136   1  15   6
  DEL PEAK 20(8P22) WILD-TYPE 177   2   9  19
D45V10, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  R0                       136                         177
  R1                         1                           2
  R2                        15                           9
  RX                         6                          19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(8P22) MUTATED                                  1     3
  DEL PEAK 20(8P22) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(8P22) MUTATED                          24   101
  DEL PEAK 20(8P22) WILD-TYPE                        26   110
D45V12, multiclass
                                  clus
vv                                 DEL PEAK 20(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    3
  BLACK OR AFRICAN AMERICAN                               24
  WHITE                                                  101
                                  clus
vv                                 DEL PEAK 20(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 26
  WHITE                                                    110
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = DEL PEAK 21(8Q11.1) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(8Q11.1) MUTATED    23   7
  DEL PEAK 21(8Q11.1) WILD-TYPE 312  80
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           30                           392 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                            7                            80 
$`DEL PEAK 21(8Q11.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-6650 
       17.79        42.28        44.91        15.52        36.53        20.61 
TCGA-A6-6654 TCGA-AA-3517 TCGA-AA-3531 TCGA-AA-3544 TCGA-AA-3666 TCGA-AA-3681 
       23.87        38.99        34.03        14.01         2.01         5.98 
TCGA-AA-3842 TCGA-AA-3989 TCGA-AA-A01D TCGA-AA-A01K TCGA-AA-A02F TCGA-AY-6196 
       37.02         7.96         0.99        31.00        39.98         0.20 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-CM-4746 TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-5540 
        5.52         6.87        37.02        17.03        13.05        13.51 
TCGA-D5-6531 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-F4-6704 TCGA-G4-6298 TCGA-G4-6625 
       17.75        49.91       131.51         1.55        23.51        91.79 

$`DEL PEAK 21(8Q11.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       23.38        35.11        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       16.04        34.65        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
       37.05         1.02        35.01        58.03        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 
       36.03         8.05        19.07        19.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99         0.99        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       13.94        19.99        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
       54.02        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
       85.05        26.99        19.04         0.99         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       36.95        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       32.05         0.99        31.07        31.07        53.00        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       24.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       20.98        34.03         2.01        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       34.03        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       42.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       15.02        15.02        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
        1.02        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK 
        1.58         1.02         0.10         0.76         0.20         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
       15.75        21.44        17.82         5.19        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       58.39         1.41         5.65        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       12.10       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        1.94         2.24         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       20.02         8.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       29.06        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
        5.03        15.02        15.02        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        11.01        12.95        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       11.51        20.19        20.42        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       15.12        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        6.18        35.87        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        46.75        47.15        52.80         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        10.52         2.79         5.98         5.59         1.32 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.19         5.49        26.99        17.29         6.64        14.76 
TCGA-RU-A8FL TCGA-WS-AB45 
       30.28        67.00 

  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                       19.200                        19.625 
[1] "0.2 - 131.5 (19.2)" "0.1 - 140.4 (19.6)"
[1] "hr=" "1.1"
D46V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 21(8Q11.1) MUTATED         2        0        0         9         1
  DEL PEAK 21(8Q11.1) WILD-TYPE      70        1       28       122         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(8Q11.1) MUTATED           0         2          1          3
  DEL PEAK 21(8Q11.1) WILD-TYPE         1        19         11         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 21(8Q11.1) MUTATED            6        3         2         1
  DEL PEAK 21(8Q11.1) WILD-TYPE         32       40        16         1
D46V3, multiclass
            clus
vv           DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  STAGE I                              2                            70
  STAGE IA                             0                             1
  STAGE II                             0                            28
  STAGE IIA                            9                           122
  STAGE IIB                            1                             7
  STAGE IIC                            0                             1
  STAGE III                            2                            19
  STAGE IIIA                           1                            11
  STAGE IIIB                           3                            52
  STAGE IIIC                           6                            32
  STAGE IV                             3                            40
  STAGE IVA                            2                            16
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 21(8Q11.1) MUTATED     0   3  24   3
  DEL PEAK 21(8Q11.1) WILD-TYPE  11  73 276  48
D46V4, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  T1                           0                            11
  T2                           3                            73
  T3                          24                           276
  T4                           3                            48
[1] 4 2
[1] 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
  DEL PEAK 21(8Q11.1) MUTATED    13   8   9
  DEL PEAK 21(8Q11.1) WILD-TYPE 243  95  70
D46V5, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  N0                          13                           243
  N1                           8                            95
  N2                           9                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 21(8Q11.1) MUTATED    20   4   1   1   2
  DEL PEAK 21(8Q11.1) WILD-TYPE 300  48   7   1  48
D46V6, multiclass
     clus
vv    DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  M0                           20                           300
  M1                            4                            48
  M1A                           1                             7
  M1B                           1                             1
  MX                            2                            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"
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    14  16
  DEL PEAK 21(8Q11.1) WILD-TYPE 193 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     14   16
  DEL PEAK 21(8Q11.1) WILD-TYPE  193  216
        clus
vv       DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  FEMALE                          14                           193
  MALE                            16                           216
[1] 2 2
[1] FALSE
D46V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    26   4
  DEL PEAK 21(8Q11.1) WILD-TYPE 352  55
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     26    4
  DEL PEAK 21(8Q11.1) WILD-TYPE  352   55
                               clus
vv                              DEL PEAK 21(8Q11.1) MUTATED
  COLON ADENOCARCINOMA                                   26
  COLON MUCINOUS ADENOCARCINOMA                           4
                               clus
vv                              DEL PEAK 21(8Q11.1) WILD-TYPE
  COLON ADENOCARCINOMA                                    352
  COLON MUCINOUS ADENOCARCINOMA                            55
[1] 2 2
[1] FALSE
D46V9, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED     0  30
  DEL PEAK 21(8Q11.1) WILD-TYPE   3 406
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED      0   30
  DEL PEAK 21(8Q11.1) WILD-TYPE    3  406
     clus
vv    DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  NO                            0                             3
  YES                          30                           406
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(8Q11.1) MUTATED    24   0   2   0
  DEL PEAK 21(8Q11.1) WILD-TYPE 289   3  22  25
D46V10, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  R0                          24                           289
  R1                           0                             3
  R2                           2                            22
  RX                           0                            25
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(8Q11.1) MUTATED                                  1     0
  DEL PEAK 21(8Q11.1) WILD-TYPE                                0    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(8Q11.1) MUTATED                           6    13
  DEL PEAK 21(8Q11.1) WILD-TYPE                        44   198
D46V12, multiclass
                                  clus
vv                                 DEL PEAK 21(8Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     13
                                  clus
vv                                 DEL PEAK 21(8Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   44
  WHITE                                                      198
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = DEL PEAK 22(9P21.3) MUTATION ANALYSIS
D47V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(9P21.3) MUTATED    46   9
  DEL PEAK 22(9P21.3) WILD-TYPE 289  78
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           55                           367 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                            9                            78 
$`DEL PEAK 22(9P21.3) MUTATED`
TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5667 TCGA-A6-6649 TCGA-A6-6651 
       43.43        36.53        14.53        29.16        24.16        21.76 
TCGA-A6-A567 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3538 TCGA-AA-3553 
       61.84        58.03         6.97        38.99        26.01        24.00 
TCGA-AA-3562 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3855 TCGA-AA-3867 
       19.99        37.05        85.05        37.02        32.05        24.03 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3972 TCGA-AA-A004 TCGA-AA-A01F 
       12.99        24.00        20.98        50.99        13.94        32.02 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6965 TCGA-AY-4070 
       31.00         1.02        40.96         4.21         0.20        16.31 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
        5.52         5.65         5.23         3.19         1.94         2.24 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-5348 TCGA-CM-6169 TCGA-CM-6170 
        3.29         0.26         8.02        22.98        13.02        15.02 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6534 
       13.05        11.08        11.01        10.06        20.19         7.92 
TCGA-D5-6898 TCGA-DM-A0XF TCGA-DM-A288 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 
        7.53        38.20        14.04        33.67         8.35        82.39 
TCGA-NH-A6GA 
        5.98 

$`DEL PEAK 22(9P21.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.76        23.38 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       17.79        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 
       15.52        37.05        37.25        16.04        34.65        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       52.44         9.63         5.03         1.02         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
       37.05         1.02        35.01        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 
        0.99        14.01        33.99        21.01        13.02        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 
       29.95        23.01        20.98        19.99        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       78.08         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
        5.98        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 
       17.98        15.95        38.99        36.95        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
        0.99        33.07        36.03         0.99        31.07        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       53.00        17.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
        2.01        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       12.00        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E 
       35.01        26.01        37.02        39.06        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05         0.07        21.37        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK 
        0.72         1.58         1.02         0.10         0.76         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        14.50        27.09         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 
        0.20        21.44        17.82         5.19         6.87        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       50.37        58.39         1.41        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        61.41        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5256 
       12.10       100.01        29.56        11.74         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
      102.44        40.34        70.16        15.62        48.20        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02         8.02        26.04        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       29.03        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.01        12.95        11.08        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        13.51        11.51        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        1.32        15.12        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A 
      131.51       135.65         7.76       139.17         6.12        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        35.87         1.55        16.31        29.59        16.24 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       55.04        51.75        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.00        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        47.15        52.80         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.98        10.52         2.79         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 
       67.00 

  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                        16.31                         19.66 
[1] "0.2 - 85.0 (16.3)"  "0.1 - 140.4 (19.7)"
[1] "hr=" "1.1"
D47V2, continuous
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 22(9P21.3) MUTATED        10        0        3        15         0
  DEL PEAK 22(9P21.3) WILD-TYPE      62        1       25       116         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(9P21.3) MUTATED           0         3          3          8
  DEL PEAK 22(9P21.3) WILD-TYPE         1        18          9         47
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 22(9P21.3) MUTATED            6        6         3         1
  DEL PEAK 22(9P21.3) WILD-TYPE         32       37        15         1
D47V3, multiclass
            clus
vv           DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  STAGE I                             10                            62
  STAGE IA                             0                             1
  STAGE II                             3                            25
  STAGE IIA                           15                           116
  STAGE IIB                            0                             8
  STAGE IIC                            0                             1
  STAGE III                            3                            18
  STAGE IIIA                           3                             9
  STAGE IIIB                           8                            47
  STAGE IIIC                           6                            32
  STAGE IV                             6                            37
  STAGE IVA                            3                            15
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 22(9P21.3) MUTATED     2  13  35   9
  DEL PEAK 22(9P21.3) WILD-TYPE   9  63 265  42
D47V4, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  T1                           2                             9
  T2                          13                            63
  T3                          35                           265
  T4                           9                            42
[1] 4 2
[1] 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
  DEL PEAK 22(9P21.3) MUTATED    29  15  14
  DEL PEAK 22(9P21.3) WILD-TYPE 227  88  65
D47V5, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  N0                          29                           227
  N1                          15                            88
  N2                          14                            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"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 22(9P21.3) MUTATED    43   7   2   1   6
  DEL PEAK 22(9P21.3) WILD-TYPE 277  45   6   1  44
D47V6, multiclass
     clus
vv    DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  M0                           43                           277
  M1                            7                            45
  M1A                           2                             6
  M1B                           1                             1
  MX                            6                            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"
D47V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    23  36
  DEL PEAK 22(9P21.3) WILD-TYPE 184 196
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     23   36
  DEL PEAK 22(9P21.3) WILD-TYPE  184  196
        clus
vv       DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  FEMALE                          23                           184
  MALE                            36                           196
[1] 2 2
[1] FALSE
D47V8, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    56   3
  DEL PEAK 22(9P21.3) WILD-TYPE 322  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     56    3
  DEL PEAK 22(9P21.3) WILD-TYPE  322   56
                               clus
vv                              DEL PEAK 22(9P21.3) MUTATED
  COLON ADENOCARCINOMA                                   56
  COLON MUCINOUS ADENOCARCINOMA                           3
                               clus
vv                              DEL PEAK 22(9P21.3) WILD-TYPE
  COLON ADENOCARCINOMA                                    322
  COLON MUCINOUS ADENOCARCINOMA                            56
[1] 2 2
[1] FALSE
D47V9, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED     0  59
  DEL PEAK 22(9P21.3) WILD-TYPE   3 377
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED      0   59
  DEL PEAK 22(9P21.3) WILD-TYPE    3  377
     clus
vv    DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  NO                            0                             3
  YES                          59                           377
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(9P21.3) MUTATED    41   1   3   3
  DEL PEAK 22(9P21.3) WILD-TYPE 272   2  21  22
D47V10, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  R0                          41                           272
  R1                           1                             2
  R2                           3                            21
  RX                           3                            22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(9P21.3) MUTATED                                  0     3
  DEL PEAK 22(9P21.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(9P21.3) MUTATED                           6    27
  DEL PEAK 22(9P21.3) WILD-TYPE                        44   184
D47V12, multiclass
                                  clus
vv                                 DEL PEAK 22(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     27
                                  clus
vv                                 DEL PEAK 22(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   44
  WHITE                                                      184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 23(10P15.3) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(10P15.3) MUTATED    60  16
  DEL PEAK 23(10P15.3) WILD-TYPE 275  71
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            76                            346 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            16                             71 
$`DEL PEAK 23(10P15.3) MUTATED`
TCGA-A6-2674 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-5659 TCGA-A6-5666 
       43.76        17.79        35.11        45.60        30.44        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU 
       29.16        22.52        25.18        23.87        61.84         9.63 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3664 TCGA-AA-3673 
        1.02         6.97        13.02        19.99        54.02        50.04 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 
       37.05        36.00        85.05         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00F 
       24.03         2.01        50.99        24.00         7.96        34.03 
TCGA-AA-A00J TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02W 
       18.05        42.02        21.99         0.99        26.01        41.00 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4323 
        1.02         0.43         0.46        14.50         0.20         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 
        5.65         5.13        65.00        62.79        29.56         3.19 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
        3.29         0.26         1.35         8.02        29.06        22.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       15.02        15.02        29.03        13.02        15.02        11.08 
TCGA-CM-6677 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 
       11.08        17.75        15.12         7.53        10.13         9.04 
TCGA-D5-6929 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6315 
       13.41        82.39        61.87        55.04        35.93        36.72 
TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A6GC TCGA-RU-A8FL 
       26.04        46.75         1.32        30.28 

$`DEL PEAK 23(10P15.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        37.02        46.65        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.04        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 
       27.09        24.13         8.38        25.08        24.16        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        52.44         5.03         1.02         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01         0.92        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       11.01         5.98        19.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       17.98        15.95        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 
       17.03        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       12.99        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       26.01        25.02        27.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       39.06        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
       21.37         4.21        56.55         0.79         0.72         1.58 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.10         0.76         0.20         0.92        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        15.75        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4681 
        6.87        75.25        50.37        58.39        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        61.41        49.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
        5.23        11.74         1.94         2.24         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        3.25         0.07         0.33         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02         8.02        26.04        27.02        13.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        15.02         5.03        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 
       14.04        11.01        12.95        13.05        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       20.19        20.42        18.25         1.32         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.50        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
       11.38        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
       44.32       131.51       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        13.38        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       13.64        13.45         6.18        35.87         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 
       19.43       107.67        28.21         8.35        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       43.07        53.62        44.68        51.75        45.11        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       36.00        26.43        22.09        13.78        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       91.79        47.15        52.80         4.11        10.98        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV 
        2.79         5.98         5.59         5.19         5.49        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
       17.29         6.64        14.76        67.00 

  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                         85.05                         140.38 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                         20.99                          19.51 
[1] "0.2 - 85.0 (21.0)"  "0.1 - 140.4 (19.5)"
[1] "hr=" "1.1"
D48V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 23(10P15.3) MUTATED        10        0        6        12         0
  DEL PEAK 23(10P15.3) WILD-TYPE      62        1       22       119         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(10P15.3) MUTATED           1         2          4         11
  DEL PEAK 23(10P15.3) WILD-TYPE         0        19          8         44
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 23(10P15.3) MUTATED            8       16         4         1
  DEL PEAK 23(10P15.3) WILD-TYPE         30       27        14         1
D48V3, multiclass
            clus
vv           DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  STAGE I                              10                             62
  STAGE IA                              0                              1
  STAGE II                              6                             22
  STAGE IIA                            12                            119
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             2                             19
  STAGE IIIA                            4                              8
  STAGE IIIB                           11                             44
  STAGE IIIC                            8                             30
  STAGE IV                             16                             27
  STAGE IVA                             4                             14
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 23(10P15.3) MUTATED     1  13  53  10
  DEL PEAK 23(10P15.3) WILD-TYPE  10  63 247  41
D48V4, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  T1                            1                             10
  T2                           13                             63
  T3                           53                            247
  T4                           10                             41
[1] 4 2
[1] 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
  DEL PEAK 23(10P15.3) MUTATED    33  23  21
  DEL PEAK 23(10P15.3) WILD-TYPE 223  80  58
D48V5, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  N0                           33                            223
  N1                           23                             80
  N2                           21                             58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 23(10P15.3) MUTATED    47  19   1   1   8
  DEL PEAK 23(10P15.3) WILD-TYPE 273  33   7   1  42
D48V6, multiclass
     clus
vv    DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  M0                            47                            273
  M1                            19                             33
  M1A                            1                              7
  M1B                            1                              1
  MX                             8                             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"
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    35  42
  DEL PEAK 23(10P15.3) WILD-TYPE 172 190
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     35   42
  DEL PEAK 23(10P15.3) WILD-TYPE  172  190
        clus
vv       DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  FEMALE                           35                            172
  MALE                             42                            190
[1] 2 2
[1] FALSE
D48V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    69   8
  DEL PEAK 23(10P15.3) WILD-TYPE 309  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     69    8
  DEL PEAK 23(10P15.3) WILD-TYPE  309   51
                               clus
vv                              DEL PEAK 23(10P15.3) MUTATED
  COLON ADENOCARCINOMA                                    69
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              DEL PEAK 23(10P15.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     309
  COLON MUCINOUS ADENOCARCINOMA                             51
[1] 2 2
[1] FALSE
D48V9, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED     2  75
  DEL PEAK 23(10P15.3) WILD-TYPE   1 361
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED      2   75
  DEL PEAK 23(10P15.3) WILD-TYPE    1  361
     clus
vv    DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  NO                             2                              1
  YES                           75                            361
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(10P15.3) MUTATED    54   0   6   5
  DEL PEAK 23(10P15.3) WILD-TYPE 259   3  18  20
D48V10, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  R0                           54                            259
  R1                            0                              3
  R2                            6                             18
  RX                            5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(10P15.3) MUTATED                                  0     3
  DEL PEAK 23(10P15.3) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(10P15.3) MUTATED                           7    42
  DEL PEAK 23(10P15.3) WILD-TYPE                        43   169
D48V12, multiclass
                                  clus
vv                                 DEL PEAK 23(10P15.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK 23(10P15.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    43
  WHITE                                                       169
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = DEL PEAK 24(10Q21.1) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(10Q21.1) MUTATED    72  20
  DEL PEAK 24(10Q21.1) WILD-TYPE 263  67
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            92                            330 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            20                             67 
$`DEL PEAK 24(10Q21.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-4107 
       37.02        17.79        35.11        45.60        34.65        32.45 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6650 
       30.44        32.71        29.16        22.52        25.18        20.61 
TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 
       23.87        61.84        52.44         9.63         1.02         6.97 
TCGA-AA-3517 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       38.99        33.99        21.01        13.02        19.99         6.05 
TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3848 TCGA-AA-3858 
       50.04        37.05        36.00        85.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3989 
       17.03        24.03         2.01        21.99        50.99         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01Q TCGA-AA-A01X TCGA-AA-A02F 
       34.03        42.02         0.99         1.02        26.01        39.98 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 
        5.03        41.00         0.79         1.02         0.43        14.50 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 
       16.31         0.20         6.87         5.65        65.00        62.79 
TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
       29.56         3.19         2.24         3.29         0.26         1.35 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
        8.02        29.06        22.03         5.03        15.02        15.02 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6531 
       29.03        13.02        15.02        11.08        11.08        17.75 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 
        7.92        15.12        17.85         7.53         9.04        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6461 TCGA-G4-6307 
       12.00        11.38        35.97       117.07        11.11        55.04 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A6GC 
       35.93        36.72        26.04        91.79        46.75         1.32 
TCGA-NH-A8F7 TCGA-RU-A8FL 
        5.19        30.28 

$`DEL PEAK 24(10Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       16.04        36.53        14.53        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 
       33.53        23.61        22.09        22.06        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        24.16        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3488 
       20.12        19.66        20.28        16.24        24.92         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        1.02         3.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
       63.98         1.02        13.02         1.02         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       37.05        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       29.00        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
       24.00        17.95        29.95        23.01        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
        5.98        19.00         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       15.95        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
       33.07        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
        2.01        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
       38.07        35.01         1.02        33.04        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R 
       39.06        51.98         2.96         2.01         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.72         1.58         0.10         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.46         0.92        27.09         0.95        15.75        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       17.82         5.19         5.52        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 
        1.41        32.94         5.13        83.80        22.36        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77        12.10       100.01         5.23        11.74 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
        1.94         3.06         2.14         3.25         0.07         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       48.20        51.32        21.99        21.14         2.93         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
      124.27        23.05        20.02        37.02         8.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.98        30.08        16.01        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        14.04        11.01        12.95        13.05 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        10.06        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       13.51        11.51        20.19        20.42        18.25         1.32 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.50        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       10.13        12.43        14.30         9.44        11.64         1.51 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      131.51       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
       26.47        81.37       119.93        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        13.38        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 
       44.68        51.75        45.11        39.42        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        26.99        17.29         6.64        14.76        67.00 

  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                        117.07                         140.38 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                        18.920                         19.625 
[1] "0.2 - 117.1 (18.9)" "0.1 - 140.4 (19.6)"
[1] "hr=" "1.2"
D49V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 24(10Q21.1) MUTATED        12        0        6        18         0
  DEL PEAK 24(10Q21.1) WILD-TYPE      60        1       22       113         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10Q21.1) MUTATED           1         2          3         13
  DEL PEAK 24(10Q21.1) WILD-TYPE         0        19          9         42
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 24(10Q21.1) MUTATED           14       16         5         1
  DEL PEAK 24(10Q21.1) WILD-TYPE         24       27        13         1
D49V3, multiclass
            clus
vv           DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  STAGE I                              12                             60
  STAGE IA                              0                              1
  STAGE II                              6                             22
  STAGE IIA                            18                            113
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             2                             19
  STAGE IIIA                            3                              9
  STAGE IIIB                           13                             42
  STAGE IIIC                           14                             24
  STAGE IV                             16                             27
  STAGE IVA                             5                             13
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 24(10Q21.1) MUTATED     2  15  66  11
  DEL PEAK 24(10Q21.1) WILD-TYPE   9  61 234  40
D49V4, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  T1                            2                              9
  T2                           15                             61
  T3                           66                            234
  T4                           11                             40
[1] 4 2
[1] 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
  DEL PEAK 24(10Q21.1) MUTATED    43  25  26
  DEL PEAK 24(10Q21.1) WILD-TYPE 213  78  53
D49V5, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  N0                           43                            213
  N1                           25                             78
  N2                           26                             53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 24(10Q21.1) MUTATED    61  19   2   1  10
  DEL PEAK 24(10Q21.1) WILD-TYPE 259  33   6   1  40
D49V6, multiclass
     clus
vv    DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  M0                            61                            259
  M1                            19                             33
  M1A                            2                              6
  M1B                            1                              1
  MX                            10                             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"
D49V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED    45  49
  DEL PEAK 24(10Q21.1) WILD-TYPE 162 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED     45   49
  DEL PEAK 24(10Q21.1) WILD-TYPE  162  183
        clus
vv       DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  FEMALE                           45                            162
  MALE                             49                            183
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED    87   7
  DEL PEAK 24(10Q21.1) WILD-TYPE 291  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED     87    7
  DEL PEAK 24(10Q21.1) WILD-TYPE  291   52
                               clus
vv                              DEL PEAK 24(10Q21.1) MUTATED
  COLON ADENOCARCINOMA                                    87
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              DEL PEAK 24(10Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     291
  COLON MUCINOUS ADENOCARCINOMA                             52
[1] 2 2
[1] FALSE
D49V9, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED     2  92
  DEL PEAK 24(10Q21.1) WILD-TYPE   1 344
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED      2   92
  DEL PEAK 24(10Q21.1) WILD-TYPE    1  344
     clus
vv    DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  NO                             2                              1
  YES                           92                            344
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(10Q21.1) MUTATED    63   1  10   6
  DEL PEAK 24(10Q21.1) WILD-TYPE 250   2  14  19
D49V10, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  R0                           63                            250
  R1                            1                              2
  R2                           10                             14
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(10Q21.1) MUTATED                                  0     4
  DEL PEAK 24(10Q21.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10Q21.1) MUTATED                          12    48
  DEL PEAK 24(10Q21.1) WILD-TYPE                        38   163
D49V12, multiclass
                                  clus
vv                                 DEL PEAK 24(10Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      48
                                  clus
vv                                 DEL PEAK 24(10Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    38
  WHITE                                                       163
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = DEL PEAK 25(10Q23.31) MUTATION ANALYSIS
D50V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(10Q23.31) MUTATED    83  20
  DEL PEAK 25(10Q23.31) WILD-TYPE 252  67
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            103                             319 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                             20                              67 
$`DEL PEAK 25(10Q23.31) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       37.02        17.79        42.28        35.11        45.60        13.94 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 
       32.45        30.44        32.71        29.16        22.52        25.18 
TCGA-A6-6649 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 
       24.16        23.87        61.84         9.63         1.02         6.97 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 
        9.07        19.07        33.99        13.02        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3692 
        6.05        54.02        50.04        11.01        37.05        36.00 
TCGA-AA-3697 TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
       85.05        36.95        33.07        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q 
       24.03         2.01        50.99         7.96        34.03        42.02 
TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6901 
        0.99        33.04        26.01        39.98        41.00         1.02 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A69D 
        0.43         0.46        14.50        16.31         5.19         5.52 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 
        5.65        65.00        62.79        29.56         3.19         2.24 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
        3.29         0.26         1.35         8.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 
       30.08         5.03        15.02        15.02        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5539 
       15.02        13.05        11.08        11.08        10.06        19.59 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 
       17.75        18.25         7.92        17.85        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D9 
       10.13         9.04        13.41       130.65        13.32       140.38 
TCGA-DM-A285 TCGA-F4-6461 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 
        6.12        11.11        16.24        33.67        55.04        36.72 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC TCGA-NH-A8F7 
       36.00        26.04        13.78        46.75         1.32         5.19 
TCGA-RU-A8FL 
       30.28 

$`DEL PEAK 25(10Q23.31) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        15.52        37.05        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       36.53        14.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 
       19.66        20.28        16.24        24.92        52.44         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        1.02         3.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 
       63.98         1.02        13.02        38.99         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       37.05        36.03         8.05        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       29.00        26.01        12.99         0.99        14.01        21.01 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        20.98        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.97         2.01        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 
       47.05        47.01        15.02         5.98        19.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 
       25.02         1.02        17.98        15.95        38.99        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
       14.93        17.03         0.99        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       12.99        24.00        33.01        26.01        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       26.01        25.02        24.00        27.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       13.94        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       17.03         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       21.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       35.01        37.02        39.06        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
        1.58         0.10         0.76         0.20         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A8YK 
        0.95        15.75         0.20        21.44        17.82         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       75.25        50.37        58.39         1.41        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        61.41        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 
      100.01         5.23        11.74         1.94         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
        3.25         0.07         0.33         0.10        17.56       102.44 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 
       40.34        70.16        15.62        48.20        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02         8.02        26.04        27.02        13.02        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       16.01        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       12.95        11.01        12.03        14.99        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       11.51        20.19        20.42         1.32        15.12         4.50 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       17.13        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
      119.70        24.43        38.20        92.75        49.91        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        13.38        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
        1.28         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
        8.35        82.39        23.51        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       53.62        44.68        51.75        45.11        39.42        35.93 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 
       26.43        22.09        35.80        26.17        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       52.80         4.11        10.98        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        5.59         5.49        26.99        17.29         6.64        14.76 
TCGA-WS-AB45 
       67.00 

  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                           0.26                            0.07 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                          18.25                           20.02 
[1] "0.3 - 140.4 (18.2)" "0.1 - 139.2 (20.0)"
[1] "hr=" "1"  
D50V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 25(10Q23.31) MUTATED        14        1        6        23         0
  DEL PEAK 25(10Q23.31) WILD-TYPE      58        0       22       108         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10Q23.31) MUTATED           1         4          6         13
  DEL PEAK 25(10Q23.31) WILD-TYPE         0        17          6         42
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 25(10Q23.31) MUTATED           11       17         5         2
  DEL PEAK 25(10Q23.31) WILD-TYPE         27       26        13         0
D50V3, multiclass
            clus
vv           DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  STAGE I                               14                              58
  STAGE IA                               1                               0
  STAGE II                               6                              22
  STAGE IIA                             23                             108
  STAGE IIB                              0                               8
  STAGE IIC                              1                               0
  STAGE III                              4                              17
  STAGE IIIA                             6                               6
  STAGE IIIB                            13                              42
  STAGE IIIC                            11                              27
  STAGE IV                              17                              26
  STAGE IVA                              5                              13
  STAGE IVB                              2                               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 25(10Q23.31) MUTATED     2  16  73  13
  DEL PEAK 25(10Q23.31) WILD-TYPE   9  60 227  38
D50V4, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  T1                             2                               9
  T2                            16                              60
  T3                            73                             227
  T4                            13                              38
[1] 4 2
[1] 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
  DEL PEAK 25(10Q23.31) MUTATED    50  30  25
  DEL PEAK 25(10Q23.31) WILD-TYPE 206  73  54
D50V5, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  N0                            50                             206
  N1                            30                              73
  N2                            25                              54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 25(10Q23.31) MUTATED    71  20   2   2  10
  DEL PEAK 25(10Q23.31) WILD-TYPE 249  32   6   0  40
D50V6, multiclass
     clus
vv    DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  M0                             71                             249
  M1                             20                              32
  M1A                             2                               6
  M1B                             2                               0
  MX                             10                              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"
D50V7, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED    52  53
  DEL PEAK 25(10Q23.31) WILD-TYPE 155 179
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     52   53
  DEL PEAK 25(10Q23.31) WILD-TYPE  155  179
        clus
vv       DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  FEMALE                            52                             155
  MALE                              53                             179
[1] 2 2
[1] FALSE
D50V8, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED    96   8
  DEL PEAK 25(10Q23.31) WILD-TYPE 282  51
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     96    8
  DEL PEAK 25(10Q23.31) WILD-TYPE  282   51
                               clus
vv                              DEL PEAK 25(10Q23.31) MUTATED
  COLON ADENOCARCINOMA                                     96
  COLON MUCINOUS ADENOCARCINOMA                             8
                               clus
vv                              DEL PEAK 25(10Q23.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      282
  COLON MUCINOUS ADENOCARCINOMA                              51
[1] 2 2
[1] FALSE
D50V9, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED     2 103
  DEL PEAK 25(10Q23.31) WILD-TYPE   1 333
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED      2  103
  DEL PEAK 25(10Q23.31) WILD-TYPE    1  333
     clus
vv    DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  NO                              2                               1
  YES                           103                             333
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 25(10Q23.31) MUTATED    74   1  10   5
  DEL PEAK 25(10Q23.31) WILD-TYPE 239   2  14  20
D50V10, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  R0                            74                             239
  R1                             1                               2
  R2                            10                              14
  RX                             5                              20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(10Q23.31) MUTATED                                  0     4
  DEL PEAK 25(10Q23.31) WILD-TYPE                                1     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10Q23.31) MUTATED                          13    55
  DEL PEAK 25(10Q23.31) WILD-TYPE                        37   156
D50V12, multiclass
                                  clus
vv                                 DEL PEAK 25(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   13
  WHITE                                                       55
                                  clus
vv                                 DEL PEAK 25(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     37
  WHITE                                                        156
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DEL PEAK 26(10Q25.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(10Q25.2) MUTATED    77  27
  DEL PEAK 26(10Q25.2) WILD-TYPE 258  60
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           104                            318 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                            27                             60 
$`DEL PEAK 26(10Q25.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 
        5.06        37.02        17.79        42.28        35.11        45.60 
TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 
       32.45        30.44        32.71        29.16        22.52        25.18 
TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.61        23.87        61.84        52.44         9.63         5.03 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3548 
        1.02         6.97         9.07        37.05        29.00        33.99 
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3680 
       13.02        19.99         6.05         2.01        50.04        11.01 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3818 
       37.05        36.00         5.03        85.05         0.99         0.99 
TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 
       36.95        33.07         0.99        17.03        24.03         2.01 
TCGA-AA-3972 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T 
       50.99         7.96        34.03        42.02         0.99        33.04 
TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 
       26.01        39.06         0.92        41.00         1.02         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4684 
        0.43        14.50        16.31         5.52         5.65        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 
       62.79        29.56         3.19         3.29         0.26         1.35 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
        2.01         8.02         8.02        29.06        22.03         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       15.02        15.02        29.03        13.02        15.02        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 
       11.08        10.06        17.75         7.92        17.85         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA 
       10.13         9.04        13.41        13.32       140.38       131.51 
TCGA-DM-A285 TCGA-DM-A28F TCGA-F4-6461 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6307 
        6.12        35.97        11.11        16.24        33.67        55.04 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A6GC 
       36.72        36.00        26.04        91.79        46.75         1.32 
TCGA-NH-A8F7 TCGA-RU-A8FL 
        5.19        30.28 

$`DEL PEAK 26(10Q25.2) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 
        5.26        46.65        43.76        43.43        23.38        44.91 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       13.94        15.52        37.05        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       36.53        14.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        24.16        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 
       19.66        20.28        16.24        24.92         1.02         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       13.02        38.99         1.02        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
        0.99        14.01        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       15.02         5.98        19.00        26.99        19.04         0.99 
TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       31.07        31.07        53.00        27.02        29.98        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       31.00         2.01        12.99        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       13.05        34.06        26.01        25.02        24.00        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       35.01         1.02        35.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         5.03        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
        0.72         1.58         0.10         0.76         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94         5.13        83.80        22.36        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        6.77        12.10       100.01         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
        2.24         3.06         2.14         3.25         0.07         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.10        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       48.20        51.32        21.99        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 
       23.05        20.02        37.02        26.04        27.02        13.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 
       22.98        30.08        16.01        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 
       14.04        11.01        12.95        13.05        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       14.99        12.26        19.59        13.51        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.42        18.25         1.32        15.12         4.50        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       12.49        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
      119.70        24.43        38.20       130.65        92.75        49.91 
TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        13.38        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 
        6.18        35.87         1.55        16.31        29.59         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       44.68        51.75        45.11        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
        4.11        10.98        10.52         2.79         5.98         5.59 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        26.99        17.29         6.64        14.76        67.00 

  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                         17.39                          20.07 
[1] "0.2 - 140.4 (17.4)" "0.1 - 139.2 (20.1)"
[1] "hr=" "1.5"
D51V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 26(10Q25.2) MUTATED        11        0        7        25         0
  DEL PEAK 26(10Q25.2) WILD-TYPE      61        1       21       106         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10Q25.2) MUTATED           1         6          4         13
  DEL PEAK 26(10Q25.2) WILD-TYPE         0        15          8         42
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 26(10Q25.2) MUTATED           12       18         5         1
  DEL PEAK 26(10Q25.2) WILD-TYPE         26       25        13         1
D51V3, multiclass
            clus
vv           DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  STAGE I                              11                             61
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            25                            106
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             6                             15
  STAGE IIIA                            4                              8
  STAGE IIIB                           13                             42
  STAGE IIIC                           12                             26
  STAGE IV                             18                             25
  STAGE IVA                             5                             13
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 26(10Q25.2) MUTATED     2  13  78  13
  DEL PEAK 26(10Q25.2) WILD-TYPE   9  63 222  38
D51V4, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  T1                            2                              9
  T2                           13                             63
  T3                           78                            222
  T4                           13                             38
[1] 4 2
[1] 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
  DEL PEAK 26(10Q25.2) MUTATED    48  31  27
  DEL PEAK 26(10Q25.2) WILD-TYPE 208  72  52
D51V5, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  N0                           48                            208
  N1                           31                             72
  N2                           27                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 26(10Q25.2) MUTATED    72  20   3   1  10
  DEL PEAK 26(10Q25.2) WILD-TYPE 248  32   5   1  40
D51V6, multiclass
     clus
vv    DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  M0                            72                            248
  M1                            20                             32
  M1A                            3                              5
  M1B                            1                              1
  MX                            10                             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"
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED    50  56
  DEL PEAK 26(10Q25.2) WILD-TYPE 157 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED     50   56
  DEL PEAK 26(10Q25.2) WILD-TYPE  157  176
        clus
vv       DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  FEMALE                           50                            157
  MALE                             56                            176
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED    97   9
  DEL PEAK 26(10Q25.2) WILD-TYPE 281  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED     97    9
  DEL PEAK 26(10Q25.2) WILD-TYPE  281   50
                               clus
vv                              DEL PEAK 26(10Q25.2) MUTATED
  COLON ADENOCARCINOMA                                    97
  COLON MUCINOUS ADENOCARCINOMA                            9
                               clus
vv                              DEL PEAK 26(10Q25.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     281
  COLON MUCINOUS ADENOCARCINOMA                             50
[1] 2 2
[1] FALSE
D51V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED     2 104
  DEL PEAK 26(10Q25.2) WILD-TYPE   1 332
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED      2  104
  DEL PEAK 26(10Q25.2) WILD-TYPE    1  332
     clus
vv    DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  NO                             2                              1
  YES                          104                            332
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(10Q25.2) MUTATED    72   1  11   5
  DEL PEAK 26(10Q25.2) WILD-TYPE 241   2  13  20
D51V10, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  R0                           72                            241
  R1                            1                              2
  R2                           11                             13
  RX                            5                             20
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(10Q25.2) MUTATED                                  0     3
  DEL PEAK 26(10Q25.2) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(10Q25.2) MUTATED                          13    53
  DEL PEAK 26(10Q25.2) WILD-TYPE                        37   158
D51V12, multiclass
                                  clus
vv                                 DEL PEAK 26(10Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      53
                                  clus
vv                                 DEL PEAK 26(10Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       158
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 27(12P13.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(12P13.2) MUTATED    40  17
  DEL PEAK 27(12P13.2) WILD-TYPE 295  70
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            57                            365 
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                            17                             70 
$`DEL PEAK 27(12P13.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 
       37.02        17.79        45.60        34.65        36.53        30.44 
TCGA-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3548 
       24.69        20.28        61.84         9.63        26.01        33.99 
TCGA-AA-3552 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3688 TCGA-AA-3858 
       13.02        78.08         2.01        50.04        19.00        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-A01F TCGA-AA-A01T 
       17.03        24.03         2.01        50.99        32.02        33.04 
TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AZ-6606 
        2.96         1.58         1.02         0.43        16.31        11.74 
TCGA-CA-5256 TCGA-CA-6715 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 
        2.14         0.07        48.20         8.02         5.03        14.04 
TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6533 
       29.03        15.02        11.01        11.08        10.06         1.32 
TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1D8 
       15.12         7.53        13.41        11.38        13.32        12.59 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 
       13.38        11.11        16.24        61.87        36.72        36.00 
TCGA-NH-A50U TCGA-NH-A8F7 TCGA-RU-A8FL 
       10.98         5.19        30.28 

$`DEL PEAK 27(12P13.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        44.91        35.11        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        16.04        14.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        20.61        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 
       20.12        19.66        16.24        24.92        52.44         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       58.03        63.98         6.97         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02         9.07        24.03        37.05        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        29.00        12.99 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
        0.99        14.01        21.01        24.00        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       23.01        20.98        19.99        13.94        19.99        61.02 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.05         6.97        54.02        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        37.05        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       38.99        36.95        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 
       33.07        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       27.02        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 
       24.00        33.01        26.01        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       13.94        38.04        19.00        30.02        34.03        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        17.03         4.01        27.02        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       17.03        14.99        21.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        35.01        26.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         0.10         0.76 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.20         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       15.75         0.20        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       32.94         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        5.23         3.19         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      102.44        40.34        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14         2.93         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       37.02         8.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        13.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        12.03        14.99        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58        12.39        10.13        12.43        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 
       24.43        38.20       130.65        92.75        49.91       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        6.12        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6463 
       60.79       117.07        98.24        95.18         8.61        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.45         6.18        35.87         1.55        16.31        29.59 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67         1.28         0.53        35.41        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       28.21         8.35        82.39        23.51        74.56        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       35.93        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        47.15        52.80         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       10.52         2.79         5.98         5.59         1.32         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        67.00 

  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                         78.08                         140.38 
  DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE 
                         15.12                          20.19 
[1] "0.1 - 78.1 (15.1)"  "0.1 - 140.4 (20.2)"
[1] "hr=" "1.9"
D52V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 27(12P13.2) MUTATED         9        0        2         9         1
  DEL PEAK 27(12P13.2) WILD-TYPE      63        1       26       122         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(12P13.2) MUTATED           0         2          1          8
  DEL PEAK 27(12P13.2) WILD-TYPE         1        19         11         47
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 27(12P13.2) MUTATED           10       10         3         0
  DEL PEAK 27(12P13.2) WILD-TYPE         28       33        15         2
D52V3, multiclass
            clus
vv           DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  STAGE I                               9                             63
  STAGE IA                              0                              1
  STAGE II                              2                             26
  STAGE IIA                             9                            122
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             2                             19
  STAGE IIIA                            1                             11
  STAGE IIIB                            8                             47
  STAGE IIIC                           10                             28
  STAGE IV                             10                             33
  STAGE IVA                             3                             15
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 27(12P13.2) MUTATED     2   8  41   6
  DEL PEAK 27(12P13.2) WILD-TYPE   9  68 259  45
D52V4, multiclass
    clus
vv   DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  T1                            2                              9
  T2                            8                             68
  T3                           41                            259
  T4                            6                             45
[1] 4 2
[1] 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
  DEL PEAK 27(12P13.2) MUTATED    25  18  14
  DEL PEAK 27(12P13.2) WILD-TYPE 231  85  65
D52V5, multiclass
    clus
vv   DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  N0                           25                            231
  N1                           18                             85
  N2                           14                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 27(12P13.2) MUTATED    34  11   2   0   9
  DEL PEAK 27(12P13.2) WILD-TYPE 286  41   6   2  41
D52V6, multiclass
     clus
vv    DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  M0                            34                            286
  M1                            11                             41
  M1A                            2                              6
  M1B                            0                              2
  MX                             9                             41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.2) MUTATED    28  29
  DEL PEAK 27(12P13.2) WILD-TYPE 179 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.2) MUTATED     28   29
  DEL PEAK 27(12P13.2) WILD-TYPE  179  203
        clus
vv       DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  FEMALE                           28                            179
  MALE                             29                            203
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.2) MUTATED    55   2
  DEL PEAK 27(12P13.2) WILD-TYPE 323  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.2) MUTATED     55    2
  DEL PEAK 27(12P13.2) WILD-TYPE  323   57
                               clus
vv                              DEL PEAK 27(12P13.2) MUTATED
  COLON ADENOCARCINOMA                                    55
  COLON MUCINOUS ADENOCARCINOMA                            2
                               clus
vv                              DEL PEAK 27(12P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     323
  COLON MUCINOUS ADENOCARCINOMA                             57
[1] 2 2
[1] FALSE
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.2) MUTATED     0  57
  DEL PEAK 27(12P13.2) WILD-TYPE   3 379
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.2) MUTATED      0   57
  DEL PEAK 27(12P13.2) WILD-TYPE    3  379
     clus
vv    DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  NO                             0                              3
  YES                           57                            379
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(12P13.2) MUTATED    40   1   4   4
  DEL PEAK 27(12P13.2) WILD-TYPE 273   2  20  21
D52V10, multiclass
    clus
vv   DEL PEAK 27(12P13.2) MUTATED DEL PEAK 27(12P13.2) WILD-TYPE
  R0                           40                            273
  R1                            1                              2
  R2                            4                             20
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(12P13.2) MUTATED                                  0     2
  DEL PEAK 27(12P13.2) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(12P13.2) MUTATED                           8    32
  DEL PEAK 27(12P13.2) WILD-TYPE                        42   179
D52V12, multiclass
                                  clus
vv                                 DEL PEAK 27(12P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 27(12P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    42
  WHITE                                                       179
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 28(14Q31.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(14Q31.1) MUTATED   111  29
  DEL PEAK 28(14Q31.1) WILD-TYPE 224  58
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                           140                            282 
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                            29                             58 
$`DEL PEAK 28(14Q31.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 
       37.02        42.28        35.11        45.60        15.52        34.65 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 
       36.53        14.53        32.45        32.91        30.44        23.61 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 
       22.52        24.13        25.08        24.16        20.61        21.76 
TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3511 
       24.69        23.87        20.28        61.84         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       38.99         9.07        24.03        19.07        19.07        34.03 
TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 
       12.99        13.02        23.01        13.94        19.99         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 
       14.01        50.04        47.01        15.02        37.05        19.00 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       85.05         0.99        25.02        36.95        37.02        17.03 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 
       31.07        17.03        24.03        18.05         2.01        12.99 
TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3989 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W 
       24.00         7.96        17.03        27.02        42.02        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X 
       21.99        15.02        32.02        31.00        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
        2.96         2.01        40.96         1.58         1.02         0.10 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
        0.43        14.50         0.95        15.75         0.20         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 
        6.87        75.25         1.41         5.65        22.36        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 
        5.23         1.94         3.06         2.14         0.07         0.26 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6163 
       48.20         2.01         8.02         8.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 
       29.03        13.02        15.02        13.05        11.08        10.06 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 
       14.99        12.26        13.51        18.25         1.32        15.12 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 
       14.30        13.41        11.38        38.20        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 
        7.50       131.51        14.04       119.93        35.97        13.38 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6297 
       29.59        33.67         1.28         0.53         8.35        82.39 
TCGA-G4-6315 TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F7 
       36.72        91.79         4.11        10.52         5.59         5.19 
TCGA-NH-A8F8 TCGA-RU-A8FL 
        5.49        30.28 

$`DEL PEAK 28(14Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       17.79        44.91        13.94        37.05        37.25        16.04 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        29.19        33.53        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 
       29.16        27.09         8.38        25.18        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 
       19.66        16.24        24.92        52.44         9.63         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3524 
       63.98         1.02        13.02         1.02        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
        8.05        29.00        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       33.99        21.01        24.00        17.95        29.95        20.98 
TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 
        0.92        47.05        11.01         5.98        36.00         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
       26.99        19.04         0.99        35.05         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 
       17.98        15.95        38.99        14.93         0.99        33.07 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 
       36.03        32.05         0.99        31.07        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       29.98        31.00        24.00        33.01        26.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 
       20.98        34.03         2.01        13.05        25.02        27.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       19.07        27.02        13.94        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        18.05         4.01         0.99        17.03 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02         0.99        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
        1.02        35.01         1.02        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       51.98        39.98         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       39.98        18.05         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        0.79         0.72         0.76         0.20         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 
       27.09        16.31        21.44        17.82         5.19        50.37 
TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
       58.39        32.94         5.13        83.80        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       61.41        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
        3.19         2.24         3.25         3.29         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        1.35        17.56       102.44        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       20.02        37.02        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       14.99        12.99        14.04        11.01        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       11.01        12.03        19.59        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       17.75         7.92        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
      119.70        24.43       130.65        92.75        49.91        12.59 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A 
       44.32       135.65         7.76       139.17         6.12        26.47 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       81.37        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       16.31        16.24        35.41        19.43       107.67        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       55.04        51.75        45.11        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        47.15        52.80        10.98         2.79         5.98 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        1.32        26.99        17.29         6.64        14.76        67.00 

  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE 
                         17.03                          20.98 
[1] "0.1 - 140.4 (17.0)" "0.1 - 139.2 (21.0)"
[1] "hr=" "1.2"
D53V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 28(14Q31.1) MUTATED        21        0        7        36         1
  DEL PEAK 28(14Q31.1) WILD-TYPE      51        1       21        95         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(14Q31.1) MUTATED           0         9          4         18
  DEL PEAK 28(14Q31.1) WILD-TYPE         1        12          8         37
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 28(14Q31.1) MUTATED           14       20        10         1
  DEL PEAK 28(14Q31.1) WILD-TYPE         24       23         8         1
D53V3, multiclass
            clus
vv           DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  STAGE I                              21                             51
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            36                             95
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             9                             12
  STAGE IIIA                            4                              8
  STAGE IIIB                           18                             37
  STAGE IIIC                           14                             24
  STAGE IV                             20                             23
  STAGE IVA                            10                              8
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 28(14Q31.1) MUTATED     6  22 102  14
  DEL PEAK 28(14Q31.1) WILD-TYPE   5  54 198  37
D53V4, multiclass
    clus
vv   DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  T1                            6                              5
  T2                           22                             54
  T3                          102                            198
  T4                           14                             37
[1] 4 2
[1] 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
  DEL PEAK 28(14Q31.1) MUTATED    72  40  32
  DEL PEAK 28(14Q31.1) WILD-TYPE 184  63  47
D53V5, multiclass
    clus
vv   DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  N0                           72                            184
  N1                           40                             63
  N2                           32                             47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 28(14Q31.1) MUTATED    97  27   3   1  14
  DEL PEAK 28(14Q31.1) WILD-TYPE 223  25   5   1  36
D53V6, multiclass
     clus
vv    DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  M0                            97                            223
  M1                            27                             25
  M1A                            3                              5
  M1B                            1                              1
  MX                            14                             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"
D53V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q31.1) MUTATED    65  79
  DEL PEAK 28(14Q31.1) WILD-TYPE 142 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q31.1) MUTATED     65   79
  DEL PEAK 28(14Q31.1) WILD-TYPE  142  153
        clus
vv       DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  FEMALE                           65                            142
  MALE                             79                            153
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q31.1) MUTATED   137   5
  DEL PEAK 28(14Q31.1) WILD-TYPE 241  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q31.1) MUTATED    137    5
  DEL PEAK 28(14Q31.1) WILD-TYPE  241   54
                               clus
vv                              DEL PEAK 28(14Q31.1) MUTATED
  COLON ADENOCARCINOMA                                   137
  COLON MUCINOUS ADENOCARCINOMA                            5
                               clus
vv                              DEL PEAK 28(14Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     241
  COLON MUCINOUS ADENOCARCINOMA                             54
[1] 2 2
[1] FALSE
D53V9, binary
                                cls
clus                               0   1
  DEL PEAK 28(14Q31.1) MUTATED     0 144
  DEL PEAK 28(14Q31.1) WILD-TYPE   3 292
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(14Q31.1) MUTATED      0  144
  DEL PEAK 28(14Q31.1) WILD-TYPE    3  292
     clus
vv    DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  NO                             0                              3
  YES                          144                            292
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 28(14Q31.1) MUTATED    96   0  11   8
  DEL PEAK 28(14Q31.1) WILD-TYPE 217   3  13  17
D53V10, multiclass
    clus
vv   DEL PEAK 28(14Q31.1) MUTATED DEL PEAK 28(14Q31.1) WILD-TYPE
  R0                           96                            217
  R1                            0                              3
  R2                           11                             13
  RX                            8                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(14Q31.1) MUTATED                                  0     4
  DEL PEAK 28(14Q31.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(14Q31.1) MUTATED                          16    67
  DEL PEAK 28(14Q31.1) WILD-TYPE                        34   144
D53V12, multiclass
                                  clus
vv                                 DEL PEAK 28(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      67
                                  clus
vv                                 DEL PEAK 28(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       144
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK 29(15Q11.2) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(15Q11.2) MUTATED   130  34
  DEL PEAK 29(15Q11.2) WILD-TYPE 205  53
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                           164                            258 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                            34                             53 
$`DEL PEAK 29(15Q11.2) MUTATED`
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 
       43.76        43.43        17.79        42.28        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       15.52        34.65        36.53        32.45        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       29.19        29.16        22.52        25.08        20.61        21.76 
TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 
       20.12        20.28        61.84        52.44         5.03         1.02 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 
        1.02         6.97        37.05        29.00        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 
       33.99        21.01        13.02        24.00        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 
       19.99         2.01        50.04        47.01        37.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3821 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       36.00        85.05         1.02        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03         0.99        36.03         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 
       24.03        27.02        29.98        12.99         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       19.00        34.03        42.02        17.03        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        32.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       41.00         1.58         1.02         0.10         0.43         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK 
       14.50        16.31         0.95        15.75         5.52         6.87 
TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 
       83.80        65.00        62.79        61.41        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 
        3.19         2.14         0.26         1.35       102.44        48.20 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 
        2.01         8.02        27.02        13.02        29.06         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 
       15.02        17.03        14.04        29.03        16.04        15.02 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 
       12.26        20.19        17.75         1.32        15.12        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A1D0 
       12.49         7.53        10.13         9.04        11.38       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
       92.75        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 
        6.12        14.04        35.97        95.18        13.38        35.87 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        16.24        33.67         1.28         0.53        35.41 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
       28.21         8.35        43.07        61.87        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V 
       36.72        36.00        91.79        46.75        10.98        10.52 
TCGA-NH-A6GC TCGA-RU-A8FL 
        1.32        30.28 

$`DEL PEAK 29(15Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 
        5.06         5.26        37.02        46.65        23.38        35.11 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 
       13.94        37.05        37.25        16.04        14.53        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 
       33.53        23.61        22.09        22.06        32.71        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        25.18        24.16        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3492 
       23.87        19.66        16.24        24.92         9.63         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
       13.02        38.99         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 
        8.05        19.07        19.07        34.03        29.00        26.01 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
        0.99        17.95        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       78.08         6.05         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.05        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 
       17.98        15.95        14.93        33.07        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       53.00        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       26.01        24.00         2.01        20.98        34.03        16.08 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       30.02        18.05        18.05        17.03         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
        0.99        21.99        34.98         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
        4.21        56.55         0.79         0.72         0.76         0.20 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09         0.20        21.44        17.82         5.19 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        22.36        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.07         0.33         0.10        17.56        40.34        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 
       23.05        20.02        37.02        26.04         8.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       22.98        30.08        16.01        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       12.00        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.01        12.95        14.99        19.59        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       20.42        18.25         7.92        17.85         4.50        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        12.43        14.30         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.41         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       38.20        49.91        44.32       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       26.47        81.37       119.93        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 
        8.61        11.11        13.64        13.45         6.18        16.31 
TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
       29.59        19.43       107.67        82.39        23.51        74.56 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       53.62        44.68        51.75        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       22.09        26.04        13.78        35.80        26.17        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 
       52.80         4.11         2.79         5.98         5.59         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.49        26.99        17.29         6.64        14.76        67.00 

  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE 
                        20.055                         19.250 
[1] "0.1 - 140.4 (20.1)" "0.1 - 139.2 (19.2)"
[1] "hr=" "1"  
D54V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 29(15Q11.2) MUTATED        27        0        7        40         2
  DEL PEAK 29(15Q11.2) WILD-TYPE      45        1       21        91         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(15Q11.2) MUTATED           0         6          8         22
  DEL PEAK 29(15Q11.2) WILD-TYPE         1        15          4         33
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 29(15Q11.2) MUTATED           19       22        11         2
  DEL PEAK 29(15Q11.2) WILD-TYPE         19       21         7         0
D54V3, multiclass
            clus
vv           DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  STAGE I                              27                             45
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            40                             91
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             6                             15
  STAGE IIIA                            8                              4
  STAGE IIIB                           22                             33
  STAGE IIIC                           19                             19
  STAGE IV                             22                             21
  STAGE IVA                            11                              7
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 29(15Q11.2) MUTATED     5  29 116  20
  DEL PEAK 29(15Q11.2) WILD-TYPE   6  47 184  31
D54V4, multiclass
    clus
vv   DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  T1                            5                              6
  T2                           29                             47
  T3                          116                            184
  T4                           20                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 29(15Q11.2) MUTATED    84  48  38
  DEL PEAK 29(15Q11.2) WILD-TYPE 172  55  41
D54V5, multiclass
    clus
vv   DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  N0                           84                            172
  N1                           48                             55
  N2                           38                             41
[1] 3 2
[1] 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 M1A M1B  MX
  DEL PEAK 29(15Q11.2) MUTATED   115  27   6   2  17
  DEL PEAK 29(15Q11.2) WILD-TYPE 205  25   2   0  33
D54V6, multiclass
     clus
vv    DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  M0                           115                            205
  M1                            27                             25
  M1A                            6                              2
  M1B                            2                              0
  MX                            17                             33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED    78  92
  DEL PEAK 29(15Q11.2) WILD-TYPE 129 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED     78   92
  DEL PEAK 29(15Q11.2) WILD-TYPE  129  140
        clus
vv       DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  FEMALE                           78                            129
  MALE                             92                            140
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED   153  15
  DEL PEAK 29(15Q11.2) WILD-TYPE 225  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED    153   15
  DEL PEAK 29(15Q11.2) WILD-TYPE  225   44
                               clus
vv                              DEL PEAK 29(15Q11.2) MUTATED
  COLON ADENOCARCINOMA                                   153
  COLON MUCINOUS ADENOCARCINOMA                           15
                               clus
vv                              DEL PEAK 29(15Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     225
  COLON MUCINOUS ADENOCARCINOMA                             44
[1] 2 2
[1] FALSE
D54V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(15Q11.2) MUTATED     3 167
  DEL PEAK 29(15Q11.2) WILD-TYPE   0 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(15Q11.2) MUTATED      3  167
  DEL PEAK 29(15Q11.2) WILD-TYPE    0  269
     clus
vv    DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  NO                             3                              0
  YES                          167                            269
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(15Q11.2) MUTATED   118   1  12   7
  DEL PEAK 29(15Q11.2) WILD-TYPE 195   2  12  18
D54V10, multiclass
    clus
vv   DEL PEAK 29(15Q11.2) MUTATED DEL PEAK 29(15Q11.2) WILD-TYPE
  R0                          118                            195
  R1                            1                              2
  R2                           12                             12
  RX                            7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(15Q11.2) MUTATED                                  1     3
  DEL PEAK 29(15Q11.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(15Q11.2) MUTATED                          15    89
  DEL PEAK 29(15Q11.2) WILD-TYPE                        35   122
D54V12, multiclass
                                  clus
vv                                 DEL PEAK 29(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                      89
                                  clus
vv                                 DEL PEAK 29(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       122
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = DEL PEAK 30(15Q15.2) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(15Q15.2) MUTATED   127  32
  DEL PEAK 30(15Q15.2) WILD-TYPE 208  55
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                           159                            263 
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                            32                             55 
$`DEL PEAK 30(15Q15.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        43.76        43.43        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       44.91        45.60        15.52        34.65        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 
       32.91        30.44        29.19        29.16        22.52        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       20.61        21.76        20.12        20.28        61.84        52.44 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 
        5.03         1.02         1.02         6.97         9.07        37.05 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99        14.01        33.99        21.01        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 
       23.01        19.99        19.99         2.01        50.04        47.01 
TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 
       11.01        37.05        19.00        36.00        85.05        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       36.95        37.02        17.03         0.99        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
        0.99        31.07        17.03        24.03        29.98        12.99 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 
        2.01        21.99        50.99        13.05        34.06        24.00 
TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       27.02        19.00        34.03        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        15.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
       41.00         1.58         1.02         0.10         0.43        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK 
       16.31         0.95        15.75         0.20         5.52         6.87 
TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 
       83.80        65.00        62.79        61.41        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 
        3.19         2.14         0.26       102.44        48.20         2.01 
TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 
        8.02        27.02        13.02        29.06         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 
       17.03        14.04        29.03        16.04        15.02        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        12.03        12.26 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 
       20.19         1.32        15.12         7.53        10.13         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       13.41        11.38       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 
      140.38       131.51         6.12        35.97        95.18        13.38 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.87         1.55        16.24        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
       35.41        28.21         8.35        61.87        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U 
       36.72        36.00        26.04        91.79        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A6GC TCGA-RU-A8FL 
       10.52         1.32        30.28 

$`DEL PEAK 30(15Q15.2) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 
        5.26        46.65        23.38        35.11        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       37.25        16.04        14.53        31.63        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        24.13         8.38 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        24.16        24.69        24.39        23.87        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 
       16.24        24.92         9.63         3.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        58.03        63.98         1.02        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
        1.02        24.03        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 
       34.03        29.00        29.00        26.01         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       29.95        20.98        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
        6.97        54.02        14.01         0.92        47.05        15.02 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.98         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       14.93        32.05        31.07        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
       31.00         2.01        24.00        33.01        26.01        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 
        2.01        20.98        34.03        16.08        26.01        25.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       19.07         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98         0.99        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
        4.21        56.55         0.79         0.72         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.46         0.92        27.09        21.44        17.82         5.19 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       75.25        50.37        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
        5.13        22.36        49.41         6.77        12.10       100.01 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 
       11.74         1.94         2.24         3.06         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
        0.07         0.33         0.10         1.35        17.56        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 
      124.27        23.05        20.02        37.02        26.04         8.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        16.01        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        12.00        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5540 
       14.04        11.01        12.95        14.99        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.42        17.75        18.25         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.50        17.13        12.49        16.14        15.58        12.39 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.43        14.30         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DA 
       10.26       119.70        24.43        38.20        49.91         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A 
       44.32       135.65         7.76       139.17        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       81.37       119.93        60.79       117.07        98.24         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 
       11.11        13.64        13.45         6.18        16.31        29.59 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       19.43       107.67        82.39        23.51        74.56        43.07 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 
       53.62        44.68        51.75        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       22.09        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 
        4.11         2.79         5.98         5.59         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
       26.99        17.29         6.64        14.76        67.00 

  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE 
                         20.12                          19.07 
[1] "0.1 - 140.4 (20.1)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1.1"
D55V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 30(15Q15.2) MUTATED        27        0        7        37         2
  DEL PEAK 30(15Q15.2) WILD-TYPE      45        1       21        94         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(15Q15.2) MUTATED           0         6          6         21
  DEL PEAK 30(15Q15.2) WILD-TYPE         1        15          6         34
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 30(15Q15.2) MUTATED           18       24        10         2
  DEL PEAK 30(15Q15.2) WILD-TYPE         20       19         8         0
D55V3, multiclass
            clus
vv           DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  STAGE I                              27                             45
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            37                             94
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             6                             15
  STAGE IIIA                            6                              6
  STAGE IIIB                           21                             34
  STAGE IIIC                           18                             20
  STAGE IV                             24                             19
  STAGE IVA                            10                              8
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 30(15Q15.2) MUTATED     5  28 112  19
  DEL PEAK 30(15Q15.2) WILD-TYPE   6  48 188  32
D55V4, multiclass
    clus
vv   DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  T1                            5                              6
  T2                           28                             48
  T3                          112                            188
  T4                           19                             32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 30(15Q15.2) MUTATED    80  49  35
  DEL PEAK 30(15Q15.2) WILD-TYPE 176  54  44
D55V5, multiclass
    clus
vv   DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  N0                           80                            176
  N1                           49                             54
  N2                           35                             44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 30(15Q15.2) MUTATED   106  28   6   2  18
  DEL PEAK 30(15Q15.2) WILD-TYPE 214  24   2   0  32
D55V6, multiclass
     clus
vv    DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  M0                           106                            214
  M1                            28                             24
  M1A                            6                              2
  M1B                            2                              0
  MX                            18                             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"
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q15.2) MUTATED    75  89
  DEL PEAK 30(15Q15.2) WILD-TYPE 132 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q15.2) MUTATED     75   89
  DEL PEAK 30(15Q15.2) WILD-TYPE  132  143
        clus
vv       DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  FEMALE                           75                            132
  MALE                             89                            143
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q15.2) MUTATED   148  14
  DEL PEAK 30(15Q15.2) WILD-TYPE 230  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q15.2) MUTATED    148   14
  DEL PEAK 30(15Q15.2) WILD-TYPE  230   45
                               clus
vv                              DEL PEAK 30(15Q15.2) MUTATED
  COLON ADENOCARCINOMA                                   148
  COLON MUCINOUS ADENOCARCINOMA                           14
                               clus
vv                              DEL PEAK 30(15Q15.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     230
  COLON MUCINOUS ADENOCARCINOMA                             45
[1] 2 2
[1] FALSE
D55V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(15Q15.2) MUTATED     3 161
  DEL PEAK 30(15Q15.2) WILD-TYPE   0 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(15Q15.2) MUTATED      3  161
  DEL PEAK 30(15Q15.2) WILD-TYPE    0  275
     clus
vv    DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  NO                             3                              0
  YES                          161                            275
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(15Q15.2) MUTATED   115   1  12   6
  DEL PEAK 30(15Q15.2) WILD-TYPE 198   2  12  19
D55V10, multiclass
    clus
vv   DEL PEAK 30(15Q15.2) MUTATED DEL PEAK 30(15Q15.2) WILD-TYPE
  R0                          115                            198
  R1                            1                              2
  R2                           12                             12
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(15Q15.2) MUTATED                                  1     2
  DEL PEAK 30(15Q15.2) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(15Q15.2) MUTATED                          16    86
  DEL PEAK 30(15Q15.2) WILD-TYPE                        34   125
D55V12, multiclass
                                  clus
vv                                 DEL PEAK 30(15Q15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                      86
                                  clus
vv                                 DEL PEAK 30(15Q15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       125
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = DEL PEAK 31(15Q21.1) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(15Q21.1) MUTATED   127  29
  DEL PEAK 31(15Q21.1) WILD-TYPE 208  58
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                           156                            266 
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                            29                             58 
$`DEL PEAK 31(15Q21.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 
       37.02        43.76        43.43        23.38        17.79        44.91 
TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       45.60        15.52        34.65        36.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 
       30.44        29.19        29.16        22.52        25.08        20.61 
TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 
       21.76        20.12        20.28        61.84         5.03         1.02 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 
        1.02         6.97         9.07        37.05        29.00        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 
       19.99        19.99         2.01        50.04        47.01        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 TCGA-AA-3841 
       37.05        19.00        36.00        85.05        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 
       37.02        17.03         0.99        33.07        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 
       31.07        17.03        24.03        29.98        12.99         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 
       21.99        50.99        13.05        34.06        24.00        27.02 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       19.00        30.02        34.03        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E 
       15.02        15.02        31.00        33.04        26.01         2.96 
TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 
       41.00         1.58         1.02         0.10         0.43        14.50 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 
       15.75         0.20         5.52         6.87        83.80        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 
       62.79        61.41        29.56         5.23         3.19         2.14 
TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 
        0.26       102.44        48.20         2.01         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       13.02        29.06         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       29.03        16.04        15.02        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6533 
       11.01        10.06        12.03        12.26        20.19         1.32 
TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       15.12         7.53        10.13         9.04        13.41        11.38 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
      130.65        92.75        13.32        12.59       140.38       131.51 
TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
        6.12        35.97        95.18        13.38        35.87         1.55 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       16.24        33.67         1.28         0.53        35.41         8.35 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 
       61.87        55.04        45.11        36.72        36.00        26.04 
TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-RU-A8FL 
       91.79        46.75        10.98        10.52         1.32        30.28 

$`DEL PEAK 31(15Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 
        5.06         5.26        46.65        42.28        35.11        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 
       37.05        37.25        16.04        14.53        31.63        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 
       23.61        22.09        22.06        32.71        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        24.16        24.69        24.39        23.87 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 
       19.66        16.24        24.92        52.44         9.63         3.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 
       37.05         1.02        35.01        58.03        63.98         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       13.02        38.99         1.02        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 
       19.07        19.07        34.03        29.00        26.01         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       17.95        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
        6.05         6.97        54.02        14.01         0.92        47.05 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       15.02         5.98         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
        0.99        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 
       15.95        14.93        32.05        31.07        53.00        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 
       24.00         2.01        20.98        34.03        16.08        26.01 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       18.05        18.05        17.03         4.01        27.02         0.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98         0.99        32.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98        39.98         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 
        4.21        56.55         0.79         0.72         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 
        0.46         0.92        27.09        16.31         0.95        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82         5.19        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 
        5.65        32.94         5.13        22.36        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       12.10       100.01        11.74         1.94         2.24         3.06 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         3.29         0.07         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56        40.34        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14         2.93       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       26.04         8.02        22.03        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        15.02        12.00        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 
       12.99        13.02        14.04        11.01        12.95        14.99 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        13.51        11.51        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        17.85         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
        1.51        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       49.91         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
       16.31        29.59        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       23.51        74.56        43.07        53.62        44.68        51.75 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 
       39.42        35.93        26.43        22.09        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        47.15        52.80         4.11         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         5.19         5.49        26.99        17.29         6.64 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       14.76        67.00 

  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE 
                        20.235                         19.070 
[1] "0.1 - 140.4 (20.2)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1.2"
D56V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 31(15Q21.1) MUTATED        25        0        7        40         3
  DEL PEAK 31(15Q21.1) WILD-TYPE      47        1       21        91         5
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(15Q21.1) MUTATED           0         6          6         19
  DEL PEAK 31(15Q21.1) WILD-TYPE         1        15          6         36
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 31(15Q21.1) MUTATED           17       23        10         2
  DEL PEAK 31(15Q21.1) WILD-TYPE         21       20         8         0
D56V3, multiclass
            clus
vv           DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  STAGE I                              25                             47
  STAGE IA                              0                              1
  STAGE II                              7                             21
  STAGE IIA                            40                             91
  STAGE IIB                             3                              5
  STAGE IIC                             0                              1
  STAGE III                             6                             15
  STAGE IIIA                            6                              6
  STAGE IIIB                           19                             36
  STAGE IIIC                           17                             21
  STAGE IV                             23                             20
  STAGE IVA                            10                              8
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 31(15Q21.1) MUTATED     4  27 111  20
  DEL PEAK 31(15Q21.1) WILD-TYPE   7  49 189  31
D56V4, multiclass
    clus
vv   DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  T1                            4                              7
  T2                           27                             49
  T3                          111                            189
  T4                           20                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 31(15Q21.1) MUTATED    82  46  34
  DEL PEAK 31(15Q21.1) WILD-TYPE 174  57  45
D56V5, multiclass
    clus
vv   DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  N0                           82                            174
  N1                           46                             57
  N2                           34                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 31(15Q21.1) MUTATED   106  27   6   2  18
  DEL PEAK 31(15Q21.1) WILD-TYPE 214  25   2   0  32
D56V6, multiclass
     clus
vv    DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  M0                           106                            214
  M1                            27                             25
  M1A                            6                              2
  M1B                            2                              0
  MX                            18                             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"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q21.1) MUTATED    73  89
  DEL PEAK 31(15Q21.1) WILD-TYPE 134 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q21.1) MUTATED     73   89
  DEL PEAK 31(15Q21.1) WILD-TYPE  134  143
        clus
vv       DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  FEMALE                           73                            134
  MALE                             89                            143
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q21.1) MUTATED   147  14
  DEL PEAK 31(15Q21.1) WILD-TYPE 231  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q21.1) MUTATED    147   14
  DEL PEAK 31(15Q21.1) WILD-TYPE  231   45
                               clus
vv                              DEL PEAK 31(15Q21.1) MUTATED
  COLON ADENOCARCINOMA                                   147
  COLON MUCINOUS ADENOCARCINOMA                           14
                               clus
vv                              DEL PEAK 31(15Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     231
  COLON MUCINOUS ADENOCARCINOMA                             45
[1] 2 2
[1] FALSE
D56V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(15Q21.1) MUTATED     3 159
  DEL PEAK 31(15Q21.1) WILD-TYPE   0 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(15Q21.1) MUTATED      3  159
  DEL PEAK 31(15Q21.1) WILD-TYPE    0  277
     clus
vv    DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  NO                             3                              0
  YES                          159                            277
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(15Q21.1) MUTATED   114   0  12   6
  DEL PEAK 31(15Q21.1) WILD-TYPE 199   3  12  19
D56V10, multiclass
    clus
vv   DEL PEAK 31(15Q21.1) MUTATED DEL PEAK 31(15Q21.1) WILD-TYPE
  R0                          114                            199
  R1                            0                              3
  R2                           12                             12
  RX                            6                             19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(15Q21.1) MUTATED                                  1     2
  DEL PEAK 31(15Q21.1) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(15Q21.1) MUTATED                          13    84
  DEL PEAK 31(15Q21.1) WILD-TYPE                        37   127
D56V12, multiclass
                                  clus
vv                                 DEL PEAK 31(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      84
                                  clus
vv                                 DEL PEAK 31(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = DEL PEAK 32(15Q22.33) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 32(15Q22.33) MUTATED   119  31
  DEL PEAK 32(15Q22.33) WILD-TYPE 216  56
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                            150                             272 
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                             31                              56 
$`DEL PEAK 32(15Q22.33) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 
       37.02        43.76        43.43        17.79        44.91        45.60 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 
       15.52        34.65        36.53        32.45        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 
       29.16        22.52        25.08        20.61        21.76        20.28 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 
       61.84         5.03         1.02         1.02         6.97         9.07 
TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       37.05        29.00        12.99        33.99        21.01        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 
       23.01        19.99        19.99         2.01        50.04        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       19.00        36.00        85.05        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
       17.03         0.99         0.99        31.07        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
       29.98        12.99         2.01        21.99        50.99        13.05 
TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       34.06        24.00        27.02        19.00        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T 
       17.03        14.99        15.02        15.02        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       26.01         2.96        41.00         1.58         1.02         0.10 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.43         0.46        14.50        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
        0.20         5.52         6.87        83.80        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 
       61.41        29.56         5.23         3.19         2.14         0.26 
TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 
      102.44        48.20         2.01         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       29.06         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       16.04        15.02        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       12.03        20.19         1.32        15.12        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 
        7.53        10.13         9.04        13.41        11.38       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
       92.75        49.91        13.32        12.59       140.38       131.51 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
        6.12        14.04        95.18        13.38        35.87         1.55 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       16.24        33.67         1.28         0.53        35.41         8.35 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 
       61.87        55.04        45.11        36.72        36.00        91.79 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-RU-A8FL 
       46.75        10.98        10.52         1.32         6.64        30.28 

$`DEL PEAK 32(15Q22.33) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
        5.06         5.26        46.65        23.38        42.28        35.11 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5656 
       13.94        37.05        37.25        16.04        14.53        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       27.09        24.13         8.38        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.39        23.87        20.12        19.66        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       52.44         9.63         3.02        37.05         1.02        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       58.03        63.98         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       24.03        36.03         8.05        19.07        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 
       29.00        26.01         0.99        14.01        24.00        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       29.95        20.98        13.94        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
        6.97        54.02        14.01         0.92        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       15.02        11.01         5.98         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
        0.99         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       17.98        15.95        14.93        33.07        36.03        32.05 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       24.00        33.01        26.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 
       34.03        16.08        26.01        25.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z TCGA-AA-A010 
       17.03         4.01        27.02         0.99        21.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 
       18.05        40.96         0.07        21.37         4.21        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
        0.79         0.72         0.76         0.20         0.92        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 
       21.44        17.82         5.19        75.25        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 
        1.41         5.65        32.94         5.13        22.36        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 
        6.77        12.10       100.01        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         3.25         3.29         0.07         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
        1.35        17.56        40.34        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       37.02        26.04         8.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 
       16.01        15.02        15.02        15.02        12.00        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       13.05        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.42        17.75        18.25         7.92        17.85         4.50 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       16.14        15.58        12.39        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       38.20         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       26.47        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
       16.31        29.59        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       23.51        74.56        43.07        53.62        44.68        51.75 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       39.42        35.93        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV 
       35.80        26.17        47.15        52.80         4.11         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.98         5.59         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       14.76        67.00 

  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE 
                         18.395                          20.070 
[1] "0.1 - 140.4 (18.4)" "0.1 - 139.2 (20.1)"
[1] "hr=" "1"  
D57V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 32(15Q22.33) MUTATED        22        0        6        37         2
  DEL PEAK 32(15Q22.33) WILD-TYPE      50        1       22        94         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(15Q22.33) MUTATED           0         5          7         18
  DEL PEAK 32(15Q22.33) WILD-TYPE         1        16          5         37
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 32(15Q22.33) MUTATED           19       22        11         1
  DEL PEAK 32(15Q22.33) WILD-TYPE         19       21         7         1
D57V3, multiclass
            clus
vv           DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  STAGE I                               22                              50
  STAGE IA                               0                               1
  STAGE II                               6                              22
  STAGE IIA                             37                              94
  STAGE IIB                              2                               6
  STAGE IIC                              0                               1
  STAGE III                              5                              16
  STAGE IIIA                             7                               5
  STAGE IIIB                            18                              37
  STAGE IIIC                            19                              19
  STAGE IV                              22                              21
  STAGE IVA                             11                               7
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 32(15Q22.33) MUTATED     5  22 109  18
  DEL PEAK 32(15Q22.33) WILD-TYPE   6  54 191  33
D57V4, multiclass
    clus
vv   DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  T1                             5                               6
  T2                            22                              54
  T3                           109                             191
  T4                            18                              33
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 32(15Q22.33) MUTATED    75  43  36
  DEL PEAK 32(15Q22.33) WILD-TYPE 181  60  43
D57V5, multiclass
    clus
vv   DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  N0                            75                             181
  N1                            43                              60
  N2                            36                              43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 32(15Q22.33) MUTATED    99  27   6   1  17
  DEL PEAK 32(15Q22.33) WILD-TYPE 221  25   2   1  33
D57V6, multiclass
     clus
vv    DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  M0                             99                             221
  M1                             27                              25
  M1A                             6                               2
  M1B                             1                               1
  MX                             17                              33
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                 cls
clus                                0   1
  DEL PEAK 32(15Q22.33) MUTATED    70  84
  DEL PEAK 32(15Q22.33) WILD-TYPE 137 148
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(15Q22.33) MUTATED     70   84
  DEL PEAK 32(15Q22.33) WILD-TYPE  137  148
        clus
vv       DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  FEMALE                            70                             137
  MALE                              84                             148
[1] 2 2
[1] FALSE
D57V8, binary
                                 cls
clus                                0   1
  DEL PEAK 32(15Q22.33) MUTATED   139  13
  DEL PEAK 32(15Q22.33) WILD-TYPE 239  46
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(15Q22.33) MUTATED    139   13
  DEL PEAK 32(15Q22.33) WILD-TYPE  239   46
                               clus
vv                              DEL PEAK 32(15Q22.33) MUTATED
  COLON ADENOCARCINOMA                                    139
  COLON MUCINOUS ADENOCARCINOMA                            13
                               clus
vv                              DEL PEAK 32(15Q22.33) WILD-TYPE
  COLON ADENOCARCINOMA                                      239
  COLON MUCINOUS ADENOCARCINOMA                              46
[1] 2 2
[1] FALSE
D57V9, binary
                                 cls
clus                                0   1
  DEL PEAK 32(15Q22.33) MUTATED     3 151
  DEL PEAK 32(15Q22.33) WILD-TYPE   0 285
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 32(15Q22.33) MUTATED      3  151
  DEL PEAK 32(15Q22.33) WILD-TYPE    0  285
     clus
vv    DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  NO                              3                               0
  YES                           151                             285
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 32(15Q22.33) MUTATED   107   1  11   6
  DEL PEAK 32(15Q22.33) WILD-TYPE 206   2  13  19
D57V10, multiclass
    clus
vv   DEL PEAK 32(15Q22.33) MUTATED DEL PEAK 32(15Q22.33) WILD-TYPE
  R0                           107                             206
  R1                             1                               2
  R2                            11                              13
  RX                             6                              19
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(15Q22.33) MUTATED                                  1     2
  DEL PEAK 32(15Q22.33) WILD-TYPE                                0     9
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(15Q22.33) MUTATED                          14    84
  DEL PEAK 32(15Q22.33) WILD-TYPE                        36   127
D57V12, multiclass
                                  clus
vv                                 DEL PEAK 32(15Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   14
  WHITE                                                       84
                                  clus
vv                                 DEL PEAK 32(15Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          9
  BLACK OR AFRICAN AMERICAN                                     36
  WHITE                                                        127
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 33(16P13.3) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(16P13.3) MUTATED    34  18
  DEL PEAK 33(16P13.3) WILD-TYPE 301  69
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                            52                            370 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                            18                             69 
$`DEL PEAK 33(16P13.3) MUTATED`
TCGA-A6-2677 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-6651 
       17.79        44.91        45.60        34.65        14.53        21.76 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3552 TCGA-AA-3664 TCGA-AA-3685 TCGA-AA-3837 
       61.84         5.03        13.02        54.02        37.05        38.99 
TCGA-AA-3841 TCGA-AA-3860 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3952 TCGA-AA-3966 
       36.95        31.07         2.01        33.01         2.01         2.01 
TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A02F TCGA-AA-A02Y TCGA-AD-A5EK 
       27.02        34.03        27.02        39.98        39.98         0.43 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 
        0.46        14.50        16.31         0.20         5.52         5.65 
TCGA-AZ-6607 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 
        3.19        13.02        22.03        22.98         5.03        15.02 
TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 
       16.04        13.02        11.01        11.01        20.19        17.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6459 TCGA-G4-6294 TCGA-G4-6626 
       49.91        12.59        44.32         8.61        28.21        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-RU-A8FL 
        4.11        10.98        26.99        30.28 

$`DEL PEAK 33(16P13.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       23.38        42.28        35.11        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        16.04        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        24.16        20.61        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       52.44         9.63         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       13.02        38.99         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        26.01        12.99         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       21.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97         2.01        14.01         0.92        50.04        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
        5.03        85.05        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       37.02        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        53.00        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05        31.00        12.99        24.00 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       26.01        24.00        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       50.99        13.05        34.06        26.01        25.02        24.00 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       19.07         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q 
       30.02        18.05        18.05        17.03         4.01        42.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 
        0.99        17.03        14.99        21.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02         0.99        32.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       26.01        37.02        39.06        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        41.00        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
        0.07        21.37         4.21        56.55         0.79         0.72 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 
        1.58         1.02         0.10         0.76         0.20         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        15.75        21.44        17.82         5.19 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        6.87        75.25        50.37        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.13        83.80        22.36        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       49.41         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.29         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02         8.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       27.02        29.06        30.08        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        29.03        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        20.42        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
        7.92        15.12        17.85         4.50        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       14.30         9.04         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        92.75        13.32       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      135.65         7.76       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        13.38        11.11        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.87         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
        1.28         0.53        35.41        19.43       107.67         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V 
       35.80        26.17        91.79        47.15        52.80        10.52 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
        2.79         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
       17.29         6.64        14.76        67.00 

  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                         61.84                         140.38 
  DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE 
                        17.770                         19.825 
[1] "0.2 - 61.8 (17.8)"  "0.1 - 140.4 (19.8)"
[1] "hr=" "2.2"
D58V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 33(16P13.3) MUTATED         3        0        3        16         2
  DEL PEAK 33(16P13.3) WILD-TYPE      69        1       25       115         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(16P13.3) MUTATED           0         0          0          9
  DEL PEAK 33(16P13.3) WILD-TYPE         1        21         12         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 33(16P13.3) MUTATED            9        6         5         0
  DEL PEAK 33(16P13.3) WILD-TYPE         29       37        13         2
D58V3, multiclass
            clus
vv           DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  STAGE I                               3                             69
  STAGE IA                              0                              1
  STAGE II                              3                             25
  STAGE IIA                            16                            115
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             0                             21
  STAGE IIIA                            0                             12
  STAGE IIIB                            9                             46
  STAGE IIIC                            9                             29
  STAGE IV                              6                             37
  STAGE IVA                             5                             13
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 33(16P13.3) MUTATED     0   3  44   7
  DEL PEAK 33(16P13.3) WILD-TYPE  11  73 256  44
D58V4, multiclass
    clus
vv   DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  T1                            0                             11
  T2                            3                             73
  T3                           44                            256
  T4                            7                             44
[1] 4 2
[1] 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
  DEL PEAK 33(16P13.3) MUTATED    25  15  14
  DEL PEAK 33(16P13.3) WILD-TYPE 231  88  65
D58V5, multiclass
    clus
vv   DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  N0                           25                            231
  N1                           15                             88
  N2                           14                             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"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 33(16P13.3) MUTATED    34   8   3   0   6
  DEL PEAK 33(16P13.3) WILD-TYPE 286  44   5   2  44
D58V6, multiclass
     clus
vv    DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  M0                            34                            286
  M1                             8                             44
  M1A                            3                              5
  M1B                            0                              2
  MX                             6                             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"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED    24  30
  DEL PEAK 33(16P13.3) WILD-TYPE 183 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED     24   30
  DEL PEAK 33(16P13.3) WILD-TYPE  183  202
        clus
vv       DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  FEMALE                           24                            183
  MALE                             30                            202
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED    47   7
  DEL PEAK 33(16P13.3) WILD-TYPE 331  52
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED     47    7
  DEL PEAK 33(16P13.3) WILD-TYPE  331   52
                               clus
vv                              DEL PEAK 33(16P13.3) MUTATED
  COLON ADENOCARCINOMA                                    47
  COLON MUCINOUS ADENOCARCINOMA                            7
                               clus
vv                              DEL PEAK 33(16P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     331
  COLON MUCINOUS ADENOCARCINOMA                             52
[1] 2 2
[1] FALSE
D58V9, binary
                                cls
clus                               0   1
  DEL PEAK 33(16P13.3) MUTATED     0  54
  DEL PEAK 33(16P13.3) WILD-TYPE   3 382
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(16P13.3) MUTATED      0   54
  DEL PEAK 33(16P13.3) WILD-TYPE    3  382
     clus
vv    DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  NO                             0                              3
  YES                           54                            382
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(16P13.3) MUTATED    40   1   3   1
  DEL PEAK 33(16P13.3) WILD-TYPE 273   2  21  24
D58V10, multiclass
    clus
vv   DEL PEAK 33(16P13.3) MUTATED DEL PEAK 33(16P13.3) WILD-TYPE
  R0                           40                            273
  R1                            1                              2
  R2                            3                             21
  RX                            1                             24
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(16P13.3) MUTATED                                  0     0
  DEL PEAK 33(16P13.3) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(16P13.3) MUTATED                          10    27
  DEL PEAK 33(16P13.3) WILD-TYPE                        40   184
D58V12, multiclass
                                  clus
vv                                 DEL PEAK 33(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      27
                                  clus
vv                                 DEL PEAK 33(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       184
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = DEL PEAK 34(16Q23.1) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(16Q23.1) MUTATED    41  16
  DEL PEAK 34(16Q23.1) WILD-TYPE 294  71
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                            57                            365 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                            16                             71 
$`DEL PEAK 34(16Q23.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2681 TCGA-A6-5660 TCGA-A6-5661 
       37.02        23.38        42.28        45.60        29.19        33.53 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-A565 TCGA-AA-3494 
       22.06        22.52        21.76        24.39        16.24         1.02 
TCGA-AA-3511 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3672 
        6.97        13.02         1.02         0.99        21.01         0.92 
TCGA-AA-3685 TCGA-AA-3831 TCGA-AA-3837 TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 
       37.05        17.98        38.99        36.03        31.07        53.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A01P 
       33.01         2.01        21.99        30.02        18.05        38.07 
TCGA-AA-A01Q TCGA-AA-A02E TCGA-AA-A02R TCGA-AA-A02W TCGA-AD-A5EK TCGA-AY-A69D 
        1.02         2.96        22.03        41.00         0.43         5.52 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-5254 
        5.65         5.13        49.41        12.10         3.19         2.24 
TCGA-CA-5797 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6169 TCGA-CM-6678 
        3.29        22.03         5.03        15.02        13.02        11.01 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-DM-A0XD TCGA-DM-A1DA TCGA-NH-A50T 
       20.19        17.75        15.12        24.43         7.50         4.11 
TCGA-NH-A50U TCGA-QG-A5Z2 TCGA-RU-A8FL 
       10.98        14.76        30.28 

$`DEL PEAK 34(16Q23.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        46.65        43.76        43.43        17.79 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       16.04        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 
       31.63        30.44        23.61        22.09        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 
       27.09        24.13         8.38        25.08        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       20.61        24.69        23.87        20.12        19.66        20.28 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
        3.02        37.05         1.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 
       17.95        29.95        23.01        20.98        19.99        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       19.99        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        19.00        36.00         5.03        85.05 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       25.02         1.02        15.95        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.99        33.07        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       17.03        24.03        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        12.99        24.00        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       26.01        25.02        24.00        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       27.02        13.94        38.04        19.00        34.03        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       17.03         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       14.99        21.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S 
       32.02        12.00        31.00        31.00        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
       33.04        35.01        26.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         5.03         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.72         1.58         1.02         0.10         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK 
       15.75         0.20        21.44        17.82         5.19         6.87 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 
       75.25        50.37        58.39         1.41        32.94        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        65.00        62.79        61.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23        11.74         1.94         3.06         2.14 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        3.25         0.07         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
       17.56       102.44        40.34        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14         2.93         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
       23.05        20.02        37.02         8.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        29.06        22.98        30.08        16.01 
TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       14.04        11.01        12.95        13.05        11.08        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.42        18.25         1.32         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
       11.64        13.41         1.51        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      139.17         6.12        14.04        26.47        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
       13.38        11.11        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        16.31        29.59        16.24        33.67         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       82.39        23.51        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       44.68        55.04        51.75        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       36.72        36.00        26.43        22.09        26.04        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 
       35.80        26.17        91.79        46.75        47.15        52.80 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.52         2.79         5.98         5.59         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-WS-AB45 
        5.49        26.99        17.29         6.64        67.00 

  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                          0.43                           0.07 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                         53.00                         140.38 
  DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE 
                         17.98                          19.99 
[1] "0.4 - 53.0 (18.0)"  "0.1 - 140.4 (20.0)"
[1] "hr=" "2"  
D59V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 34(16Q23.1) MUTATED        10        0        5        17         2
  DEL PEAK 34(16Q23.1) WILD-TYPE      62        1       23       114         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(16Q23.1) MUTATED           0         3          0          8
  DEL PEAK 34(16Q23.1) WILD-TYPE         1        18         12         47
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 34(16Q23.1) MUTATED            3        6         4         0
  DEL PEAK 34(16Q23.1) WILD-TYPE         35       37        14         2
D59V3, multiclass
            clus
vv           DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  STAGE I                              10                             62
  STAGE IA                              0                              1
  STAGE II                              5                             23
  STAGE IIA                            17                            114
  STAGE IIB                             2                              6
  STAGE IIC                             0                              1
  STAGE III                             3                             18
  STAGE IIIA                            0                             12
  STAGE IIIB                            8                             47
  STAGE IIIC                            3                             35
  STAGE IV                              6                             37
  STAGE IVA                             4                             14
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 34(16Q23.1) MUTATED     0  10  39   9
  DEL PEAK 34(16Q23.1) WILD-TYPE  11  66 261  42
D59V4, multiclass
    clus
vv   DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  T1                            0                             11
  T2                           10                             66
  T3                           39                            261
  T4                            9                             42
[1] 4 2
[1] 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
  DEL PEAK 34(16Q23.1) MUTATED    36  14   8
  DEL PEAK 34(16Q23.1) WILD-TYPE 220  89  71
D59V5, multiclass
    clus
vv   DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  N0                           36                            220
  N1                           14                             89
  N2                            8                             71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 34(16Q23.1) MUTATED    40   7   3   0   8
  DEL PEAK 34(16Q23.1) WILD-TYPE 280  45   5   2  42
D59V6, multiclass
     clus
vv    DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  M0                            40                            280
  M1                             7                             45
  M1A                            3                              5
  M1B                            0                              2
  MX                             8                             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"
D59V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED    31  27
  DEL PEAK 34(16Q23.1) WILD-TYPE 176 205
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED     31   27
  DEL PEAK 34(16Q23.1) WILD-TYPE  176  205
        clus
vv       DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  FEMALE                           31                            176
  MALE                             27                            205
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED    48  10
  DEL PEAK 34(16Q23.1) WILD-TYPE 330  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED     48   10
  DEL PEAK 34(16Q23.1) WILD-TYPE  330   49
                               clus
vv                              DEL PEAK 34(16Q23.1) MUTATED
  COLON ADENOCARCINOMA                                    48
  COLON MUCINOUS ADENOCARCINOMA                           10
                               clus
vv                              DEL PEAK 34(16Q23.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     330
  COLON MUCINOUS ADENOCARCINOMA                             49
[1] 2 2
[1] FALSE
D59V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(16Q23.1) MUTATED     0  58
  DEL PEAK 34(16Q23.1) WILD-TYPE   3 378
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(16Q23.1) MUTATED      0   58
  DEL PEAK 34(16Q23.1) WILD-TYPE    3  378
     clus
vv    DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  NO                             0                              3
  YES                           58                            378
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(16Q23.1) MUTATED    40   0   2   4
  DEL PEAK 34(16Q23.1) WILD-TYPE 273   3  22  21
D59V10, multiclass
    clus
vv   DEL PEAK 34(16Q23.1) MUTATED DEL PEAK 34(16Q23.1) WILD-TYPE
  R0                           40                            273
  R1                            0                              3
  R2                            2                             22
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(16Q23.1) MUTATED                                  0     2
  DEL PEAK 34(16Q23.1) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(16Q23.1) MUTATED                          11    22
  DEL PEAK 34(16Q23.1) WILD-TYPE                        39   189
D59V12, multiclass
                                  clus
vv                                 DEL PEAK 34(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      22
                                  clus
vv                                 DEL PEAK 34(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       189
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = DEL PEAK 35(17P12) MUTATION ANALYSIS
D60V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 35(17P12) MUTATED   186  52
  DEL PEAK 35(17P12) WILD-TYPE 149  35
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                         238                          184 
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                          52                           35 
$`DEL PEAK 35(17P12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        43.76        43.43        17.79        42.28 
TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       35.11        45.60        15.52        37.05        37.25        34.65 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 
       32.71        29.16        27.09        22.52        24.13        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       24.16        20.61        24.69        23.87        20.28        61.84 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 
        5.03         1.02         1.02        37.05         1.02         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        1.02        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       24.00        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.05         2.01        14.01        50.04        47.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3811 
        5.98        37.05        19.00        36.00        85.05         0.99 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 
       25.02        38.99        36.95        37.02         0.99        33.07 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
       32.05         0.99        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 
       29.98        18.05         2.01        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 
       34.03        21.99        16.08        50.99        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L 
       24.00        27.02         7.96        19.00        34.03        17.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A01C 
       27.02        42.02        17.03        14.99        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
        0.99        32.02        12.00        31.00         1.02        33.04 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W 
       37.02         2.96        39.98         2.01         5.03        41.00 
TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        21.37         4.21         0.79         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        0.10         0.20         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 
        0.95        15.75         0.20         5.52        75.25         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
        5.65         5.13        83.80        22.36        65.00        61.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23         3.19         1.94         2.24 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        2.14         3.29         0.07         0.26         1.35       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       48.20        21.99         2.01         8.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       13.02        29.06        22.03         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6170 
       17.03        29.03        21.99        14.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.01        13.05        11.08        10.06        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        13.51        11.51        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
        7.92        15.12        17.13        12.49        15.58         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       10.13        12.43        14.30         9.04        13.41        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        92.75        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
      140.38        44.32       131.51       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 
       26.47       119.93        35.97       117.07        13.38        11.11 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6298 
       16.31        16.24        33.67         1.28         8.35        23.51 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       61.87        44.68        55.04        45.11        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50U 
       36.72        36.00        26.43        91.79        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.52         5.98         5.59         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       26.99        17.29         6.64        30.28 

$`DEL PEAK 35(17P12) WILD-TYPE`
TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 
        5.26        46.65        23.38        44.91        13.94        16.04 
TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 
       36.53        33.53        23.61        22.09        22.06         8.38 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       25.08        21.76        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 
       24.92        52.44         9.63         3.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       63.98        13.02         1.02         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
       34.03        29.00        26.01         0.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
       20.98         6.97        54.02         0.92        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
       11.01         5.03        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3846 
        0.99         1.02        17.98        15.95        14.93        17.03 
TCGA-AA-3854 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 
       36.03        31.07        53.00        31.00        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 
       26.01        24.00         2.01        13.05        25.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        13.94        38.04        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P 
        4.01         0.99        34.98        15.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        35.01        35.01        26.01        39.06        51.98 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
        0.92        22.03        39.98        18.05         0.07        56.55 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
        0.72         0.76         0.92        27.09        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5403 
        5.19         6.87        50.37        58.39        32.94        62.79 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 
       49.41         6.77       100.01        11.74         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       37.02        26.04        22.98        30.08        16.01        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6171 
       15.02        12.00        14.04        16.04        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 
       12.95        11.08        11.01        12.03        20.19        20.42 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       17.85         4.50        16.14        12.39         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1DA 
        1.51        12.00        10.26       119.70        49.91         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
      135.65         7.76        81.37        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        13.64        13.45         6.18        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       29.59         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 
       82.39        74.56        43.07        53.62        51.75        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        47.15        52.80 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-QG-A5Z2 TCGA-WS-AB45 
        4.11         2.79        14.76        67.00 

  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                        0.07                         0.07 
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                      140.38                       135.65 
  DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE 
                       19.00                        20.07 
[1] "0.1 - 140.4 (19.0)" "0.1 - 135.7 (20.1)"
[1] "hr=" "1.3"
D60V2, continuous
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 35(17P12) MUTATED        35        0       13        55         1
  DEL PEAK 35(17P12) WILD-TYPE      37        1       15        76         7
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(17P12) MUTATED           1        12         11         34
  DEL PEAK 35(17P12) WILD-TYPE         0         9          1         21
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 35(17P12) MUTATED           29       33        13         2
  DEL PEAK 35(17P12) WILD-TYPE          9       10         5         0
D60V3, multiclass
            clus
vv           DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  STAGE I                            35                           37
  STAGE IA                            0                            1
  STAGE II                           13                           15
  STAGE IIA                          55                           76
  STAGE IIB                           1                            7
  STAGE IIC                           1                            0
  STAGE III                          12                            9
  STAGE IIIA                         11                            1
  STAGE IIIB                         34                           21
  STAGE IIIC                         29                            9
  STAGE IV                           33                           10
  STAGE IVA                          13                            5
  STAGE IVB                           2                            0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  DEL PEAK 35(17P12) MUTATED     7  40 169  29
  DEL PEAK 35(17P12) WILD-TYPE   4  36 131  22
D60V4, multiclass
    clus
vv   DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  T1                          7                            4
  T2                         40                           36
  T3                        169                          131
  T4                         29                           22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  DEL PEAK 35(17P12) MUTATED   118  69  57
  DEL PEAK 35(17P12) WILD-TYPE 138  34  22
D60V5, multiclass
    clus
vv   DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  N0                        118                          138
  N1                         69                           34
  N2                         57                           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                            M0  M1 M1A M1B  MX
  DEL PEAK 35(17P12) MUTATED   168  40   6   2  26
  DEL PEAK 35(17P12) WILD-TYPE 152  12   2   0  24
D60V6, multiclass
     clus
vv    DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  M0                         168                          152
  M1                          40                           12
  M1A                          6                            2
  M1B                          2                            0
  MX                          26                           24
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                              cls
clus                             0   1
  DEL PEAK 35(17P12) MUTATED   109 136
  DEL PEAK 35(17P12) WILD-TYPE  98  96
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(17P12) MUTATED    109  136
  DEL PEAK 35(17P12) WILD-TYPE   98   96
        clus
vv       DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  FEMALE                        109                           98
  MALE                          136                           96
[1] 2 2
[1] FALSE
D60V8, binary
                              cls
clus                             0   1
  DEL PEAK 35(17P12) MUTATED   227  16
  DEL PEAK 35(17P12) WILD-TYPE 151  43
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(17P12) MUTATED    227   16
  DEL PEAK 35(17P12) WILD-TYPE  151   43
                               clus
vv                              DEL PEAK 35(17P12) MUTATED
  COLON ADENOCARCINOMA                                 227
  COLON MUCINOUS ADENOCARCINOMA                         16
                               clus
vv                              DEL PEAK 35(17P12) WILD-TYPE
  COLON ADENOCARCINOMA                                   151
  COLON MUCINOUS ADENOCARCINOMA                           43
[1] 2 2
[1] FALSE
D60V9, binary
                              cls
clus                             0   1
  DEL PEAK 35(17P12) MUTATED     3 242
  DEL PEAK 35(17P12) WILD-TYPE   0 194
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 35(17P12) MUTATED      3  242
  DEL PEAK 35(17P12) WILD-TYPE    0  194
     clus
vv    DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  NO                           3                            0
  YES                        242                          194
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 35(17P12) MUTATED   171   1  17  10
  DEL PEAK 35(17P12) WILD-TYPE 142   2   7  15
D60V10, multiclass
    clus
vv   DEL PEAK 35(17P12) MUTATED DEL PEAK 35(17P12) WILD-TYPE
  R0                        171                          142
  R1                          1                            2
  R2                         17                            7
  RX                         10                           15
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(17P12) MUTATED                                  0     6
  DEL PEAK 35(17P12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(17P12) MUTATED                          29   119
  DEL PEAK 35(17P12) WILD-TYPE                        21    92
D60V12, multiclass
                                  clus
vv                                 DEL PEAK 35(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     6
  BLACK OR AFRICAN AMERICAN                                29
  WHITE                                                   119
                                  clus
vv                                 DEL PEAK 35(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                      92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = DEL PEAK 36(17Q24.3) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(17Q24.3) MUTATED    49  18
  DEL PEAK 36(17Q24.3) WILD-TYPE 286  69
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                            67                            355 
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                            18                             69 
$`DEL PEAK 36(17Q24.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-6138 
       37.02        43.76        37.05        32.45        31.63        22.52 
TCGA-A6-6648 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3560 
       25.18        24.16        24.03        12.99        21.01        19.99 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3811 
        6.05         2.01        50.04        37.05        19.00         0.99 
TCGA-AA-3842 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3976 TCGA-AA-3989 
       37.02        31.07        27.02        24.00        26.01         7.96 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E 
       34.03        42.02         0.99        32.02        33.04         2.96 
TCGA-AA-A02F TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-6196 TCGA-AY-A69D 
       39.98         1.58         1.02         0.20         0.20         5.52 
TCGA-AY-A8YK TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4747 
        6.87        12.10         3.29         0.26        48.20         8.02 
TCGA-CM-4751 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6170 TCGA-D5-5537 TCGA-D5-6534 
       27.02         5.03        15.02        15.02        14.99         7.92 
TCGA-D5-6539 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D8 
       12.49        13.41        11.38        38.20       130.65        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6569 
      140.38        44.32         7.76       117.07        13.38        13.45 
TCGA-F4-6704 TCGA-F4-6809 TCGA-G4-6295 TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GC 
        1.55         1.28         8.35        10.98         5.98         1.32 
TCGA-QG-A5YV 
       26.99 

$`DEL PEAK 36(17Q24.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.25        16.04        34.65        36.53        14.53        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        24.13         8.38        25.08 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       20.61        21.76        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         1.02         3.02         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        35.01        58.03        63.98         6.97         1.02 
TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3524 
       13.02        38.99         1.02         9.07        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
        8.05        19.07        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       26.01         0.99        14.01        33.99        13.02        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.97        54.02        14.01         0.92 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 
       47.05        47.01        15.02        11.01         5.98        36.00 
TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.03        85.05        26.99        19.04         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       36.95        14.93        17.03         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        53.00        17.03        24.03 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 
       29.98        18.05        31.00         2.01        12.99        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       26.01        24.00         2.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       21.99        16.08        50.99        13.05        34.06        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02         0.99        17.03        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        15.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       39.06        51.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       41.00        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         0.10         0.76 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
        0.43         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
        0.95        15.75        21.44        17.82         5.19        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       83.80        22.36        65.00        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77       100.01        29.56         5.23        11.74         3.19 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
        1.94         2.24         3.06         2.14         3.25         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.33         0.10         1.35        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        2.01       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       16.01        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.01        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       13.51        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
        1.32        15.12        17.85         4.50        17.13        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       15.58         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
        9.04         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA 
      119.70        24.43        92.75        49.91        13.32         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
      131.51       135.65       139.17         6.12        14.04        26.47 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        35.97        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
        8.61        11.11        13.64         6.18        35.87        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24        33.67         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
      107.67        28.21        82.39        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       61.87        53.62        44.68        55.04        51.75        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       39.42        35.93        36.72        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       47.15        52.80         4.11        10.52         2.79         5.59 
TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
        5.19         5.49        17.29         6.64        14.76        30.28 
TCGA-WS-AB45 
       67.00 

  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE 
                         15.02                          20.02 
[1] "0.2 - 140.4 (15.0)" "0.1 - 139.2 (20.0)"
[1] "hr=" "1.6"
D61V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 36(17Q24.3) MUTATED         9        0        4        10         0
  DEL PEAK 36(17Q24.3) WILD-TYPE      63        1       24       121         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(17Q24.3) MUTATED           0         3          3          7
  DEL PEAK 36(17Q24.3) WILD-TYPE         1        18          9         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 36(17Q24.3) MUTATED           11       10         7         1
  DEL PEAK 36(17Q24.3) WILD-TYPE         27       33        11         1
D61V3, multiclass
            clus
vv           DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  STAGE I                               9                             63
  STAGE IA                              0                              1
  STAGE II                              4                             24
  STAGE IIA                            10                            121
  STAGE IIB                             0                              8
  STAGE IIC                             0                              1
  STAGE III                             3                             18
  STAGE IIIA                            3                              9
  STAGE IIIB                            7                             48
  STAGE IIIC                           11                             27
  STAGE IV                             10                             33
  STAGE IVA                             7                             11
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 36(17Q24.3) MUTATED     0  11  45  12
  DEL PEAK 36(17Q24.3) WILD-TYPE  11  65 255  39
D61V4, multiclass
    clus
vv   DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  T1                            0                             11
  T2                           11                             65
  T3                           45                            255
  T4                           12                             39
[1] 4 2
[1] 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
  DEL PEAK 36(17Q24.3) MUTATED    27  23  18
  DEL PEAK 36(17Q24.3) WILD-TYPE 229  80  61
D61V5, multiclass
    clus
vv   DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  N0                           27                            229
  N1                           23                             80
  N2                           18                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 36(17Q24.3) MUTATED    39  12   5   1   9
  DEL PEAK 36(17Q24.3) WILD-TYPE 281  40   3   1  41
D61V6, multiclass
     clus
vv    DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  M0                            39                            281
  M1                            12                             40
  M1A                            5                              3
  M1B                            1                              1
  MX                             9                             41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(17Q24.3) MUTATED    28  40
  DEL PEAK 36(17Q24.3) WILD-TYPE 179 192
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17Q24.3) MUTATED     28   40
  DEL PEAK 36(17Q24.3) WILD-TYPE  179  192
        clus
vv       DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  FEMALE                           28                            179
  MALE                             40                            192
[1] 2 2
[1] FALSE
D61V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(17Q24.3) MUTATED    58  10
  DEL PEAK 36(17Q24.3) WILD-TYPE 320  49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17Q24.3) MUTATED     58   10
  DEL PEAK 36(17Q24.3) WILD-TYPE  320   49
                               clus
vv                              DEL PEAK 36(17Q24.3) MUTATED
  COLON ADENOCARCINOMA                                    58
  COLON MUCINOUS ADENOCARCINOMA                           10
                               clus
vv                              DEL PEAK 36(17Q24.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     320
  COLON MUCINOUS ADENOCARCINOMA                             49
[1] 2 2
[1] FALSE
D61V9, binary
                                cls
clus                               0   1
  DEL PEAK 36(17Q24.3) MUTATED     0  68
  DEL PEAK 36(17Q24.3) WILD-TYPE   3 368
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(17Q24.3) MUTATED      0   68
  DEL PEAK 36(17Q24.3) WILD-TYPE    3  368
     clus
vv    DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  NO                             0                              3
  YES                           68                            368
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(17Q24.3) MUTATED    43   0   6   4
  DEL PEAK 36(17Q24.3) WILD-TYPE 270   3  18  21
D61V10, multiclass
    clus
vv   DEL PEAK 36(17Q24.3) MUTATED DEL PEAK 36(17Q24.3) WILD-TYPE
  R0                           43                            270
  R1                            0                              3
  R2                            6                             18
  RX                            4                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(17Q24.3) MUTATED                                  1     2
  DEL PEAK 36(17Q24.3) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(17Q24.3) MUTATED                           8    34
  DEL PEAK 36(17Q24.3) WILD-TYPE                        42   177
D61V12, multiclass
                                  clus
vv                                 DEL PEAK 36(17Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 36(17Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    42
  WHITE                                                       177
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = DEL PEAK 37(18P11.31) MUTATION ANALYSIS
D62V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 37(18P11.31) MUTATED   187  46
  DEL PEAK 37(18P11.31) WILD-TYPE 148  41
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                            233                             189 
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                             46                              41 
$`DEL PEAK 37(18P11.31) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 
       32.91        30.44        29.19        23.61        22.09        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       29.16        27.09        24.13        25.08        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       21.76        24.69        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         1.02         1.02        37.05         1.02 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3526 TCGA-AA-3530 
        6.97        38.99         9.07        37.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 
       34.03        29.00        26.01        14.01        33.99        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 
       24.00        23.01        19.99        13.94        19.99        78.08 
TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
        6.05         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 
       37.05        19.00        36.00        85.05        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       18.05        12.99        24.00        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        26.01        24.00 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O 
        7.96        13.94        19.00        34.03        17.03        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       42.02        14.99        21.99        15.02        15.02        32.02 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       31.00         1.02        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 
        2.01         5.03        41.00        40.96         4.21         0.79 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        1.58         1.02         0.10         0.20         0.43        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
        0.95        15.75         5.19         5.52         6.87        75.25 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 
       12.10        29.56         5.23         1.94         2.24         2.14 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 
        3.29         0.07         0.26         1.35        48.20        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        2.01         8.02         8.02        13.02        29.06        22.03 
TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
       30.08         5.03        15.02        17.03        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 
       16.04        21.99        13.02        15.02        11.01        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        14.99        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 
       11.51        20.19        18.25         1.32        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
       12.49         7.53        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 
       11.38        24.43        38.20       130.65        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F 
      140.38        44.32       139.17        26.47       119.93        35.97 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 
      117.07        95.18        13.38        11.11        13.45         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       16.31        29.59        16.24        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
       35.41        28.21         8.35        82.39        23.51        61.87 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       55.04        45.11        36.72        36.00        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F7 
       47.15         4.11        10.98        10.52         1.32         5.19 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
        5.49        26.99        17.29         6.64        30.28 

$`DEL PEAK 37(18P11.31) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2686 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5665 
       46.65        23.38        16.04        31.63        33.53        22.06 
TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       22.52         8.38        24.16        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       16.24        24.92         3.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
        1.02        13.02         1.02        24.03        36.03         8.05 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 
       29.00        12.99         0.99        21.01        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 
       20.98        61.02         6.97        54.02         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       11.01         5.98         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       36.03        32.05        53.00        29.98        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 
       33.01        26.01        24.00         2.01         2.01        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       27.02        19.07        27.02        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D 
       18.05         4.01         0.99        17.03        34.98         0.99 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        39.06        51.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       18.05         0.07        21.37        56.55         0.72         0.76 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 
        0.46         0.92        27.09        16.31         0.20        21.44 
TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 
       17.82        50.37        58.39         1.41        32.94        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
       49.41         6.77       100.01        11.74         3.19         3.06 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        3.25         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       23.05        20.02        37.02        26.04        27.02        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 
       16.01        15.02        15.02        15.02        12.00        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5539 
       12.99        14.04        12.95        13.05        11.08        19.59 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 
       20.42        17.75         7.92        15.12         4.50        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       15.58        12.39        10.13         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA 
       12.00        10.26       119.70        92.75        49.91         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C 
      131.51       135.65         7.76         6.12        14.04        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       60.79        98.24         8.61        13.64         6.18        35.87 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       19.43       107.67        74.56        43.07        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       51.75        39.42        35.93        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA 
       13.78        35.80        26.17        52.80         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-WS-AB45 
        5.59        14.76        67.00 

  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                         140.38                          135.65 
  DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE 
                          19.07                           19.66 
[1] "0.1 - 140.4 (19.1)" "0.1 - 135.7 (19.7)"
[1] "hr=" "1"  
D62V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 37(18P11.31) MUTATED        35        0       10        65         2
  DEL PEAK 37(18P11.31) WILD-TYPE      37        1       18        66         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(18P11.31) MUTATED           1         9          8         32
  DEL PEAK 37(18P11.31) WILD-TYPE         0        12          4         23
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 37(18P11.31) MUTATED           22       32        16         1
  DEL PEAK 37(18P11.31) WILD-TYPE         16       11         2         1
D62V3, multiclass
            clus
vv           DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  STAGE I                               35                              37
  STAGE IA                               0                               1
  STAGE II                              10                              18
  STAGE IIA                             65                              66
  STAGE IIB                              2                               6
  STAGE IIC                              1                               0
  STAGE III                              9                              12
  STAGE IIIA                             8                               4
  STAGE IIIB                            32                              23
  STAGE IIIC                            22                              16
  STAGE IV                              32                              11
  STAGE IVA                             16                               2
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 37(18P11.31) MUTATED     7  40 163  29
  DEL PEAK 37(18P11.31) WILD-TYPE   4  36 137  22
D62V4, multiclass
    clus
vv   DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  T1                             7                               4
  T2                            40                              36
  T3                           163                             137
  T4                            29                              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 37(18P11.31) MUTATED   126  66  46
  DEL PEAK 37(18P11.31) WILD-TYPE 130  37  33
D62V5, multiclass
    clus
vv   DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  N0                           126                             130
  N1                            66                              37
  N2                            46                              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                               M0  M1 M1A M1B  MX
  DEL PEAK 37(18P11.31) MUTATED   160  40   8   1  27
  DEL PEAK 37(18P11.31) WILD-TYPE 160  12   0   1  23
D62V6, multiclass
     clus
vv    DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  M0                            160                             160
  M1                             40                              12
  M1A                             8                               0
  M1B                             1                               1
  MX                             27                              23
[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"
D62V7, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18P11.31) MUTATED   111 128
  DEL PEAK 37(18P11.31) WILD-TYPE  96 104
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18P11.31) MUTATED    111  128
  DEL PEAK 37(18P11.31) WILD-TYPE   96  104
        clus
vv       DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  FEMALE                           111                              96
  MALE                             128                             104
[1] 2 2
[1] FALSE
D62V8, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18P11.31) MUTATED   227  10
  DEL PEAK 37(18P11.31) WILD-TYPE 151  49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18P11.31) MUTATED    227   10
  DEL PEAK 37(18P11.31) WILD-TYPE  151   49
                               clus
vv                              DEL PEAK 37(18P11.31) MUTATED
  COLON ADENOCARCINOMA                                    227
  COLON MUCINOUS ADENOCARCINOMA                            10
                               clus
vv                              DEL PEAK 37(18P11.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      151
  COLON MUCINOUS ADENOCARCINOMA                              49
[1] 2 2
[1] FALSE
D62V9, binary
                                 cls
clus                                0   1
  DEL PEAK 37(18P11.31) MUTATED     3 236
  DEL PEAK 37(18P11.31) WILD-TYPE   0 200
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 37(18P11.31) MUTATED      3  236
  DEL PEAK 37(18P11.31) WILD-TYPE    0  200
     clus
vv    DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  NO                              3                               0
  YES                           236                             200
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 37(18P11.31) MUTATED   168   0  18  11
  DEL PEAK 37(18P11.31) WILD-TYPE 145   3   6  14
D62V10, multiclass
    clus
vv   DEL PEAK 37(18P11.31) MUTATED DEL PEAK 37(18P11.31) WILD-TYPE
  R0                           168                             145
  R1                             0                               3
  R2                            18                               6
  RX                            11                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(18P11.31) MUTATED                                  1     6
  DEL PEAK 37(18P11.31) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(18P11.31) MUTATED                          30   116
  DEL PEAK 37(18P11.31) WILD-TYPE                        20    95
D62V12, multiclass
                                  clus
vv                                 DEL PEAK 37(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   30
  WHITE                                                      116
                                  clus
vv                                 DEL PEAK 37(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     20
  WHITE                                                         95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = DEL PEAK 38(18Q12.2) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 38(18Q12.2) MUTATED   206  54
  DEL PEAK 38(18Q12.2) WILD-TYPE 129  33
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                           260                            162 
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                            54                             33 
$`DEL PEAK 38(18Q12.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       32.45        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 
       32.71        29.16        27.09        22.52        24.13        25.18 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       20.61        21.76        23.87        20.28        61.84        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        9.63         5.03         1.02         1.02        37.05         1.02 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
        6.97        38.99         9.07        24.03        37.05        36.03 
TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       19.07        19.07        34.03        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3556 
       14.01        33.99        21.01        13.02        24.00        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 
       19.99        13.94        19.99        61.02        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        2.01        14.01        50.04        47.01        15.02         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 
       37.05        19.00        36.00        85.05        25.02        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 
       36.95        37.02        14.93        17.03         0.99        33.07 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 
       29.98        18.05        12.99        24.00         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03        21.99        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       26.01        24.00        27.02         7.96        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 
       18.05        42.02        17.03        14.99        21.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       15.02         0.99        32.02        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
        0.92        41.00        40.96         4.21         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 
        1.02         0.10         0.76         0.20         0.43         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
       14.50        16.31        15.75         5.19         5.52         6.87 
TCGA-AZ-4308 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       75.25         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 
       61.41        12.10        29.56         5.23         1.94         2.24 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        2.14         3.29         0.07         0.26         1.35       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       48.20        21.99         2.01         8.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 
       13.02        29.06        22.03        30.08         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
       17.03        14.04        29.03        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        11.01        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        14.99        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       20.19        18.25         1.32        17.85        17.13        12.49 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       15.58         7.53        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       13.41        11.38        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
      131.51       139.17         6.12        14.04        26.47       119.93 
TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 
      117.07        95.18         8.61        13.38        11.11        13.45 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24         1.28         0.53 
TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
       35.41        28.21         8.35        82.39        23.51        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       36.00        91.79        46.75        47.15         4.11        10.98 
TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       10.52         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-RU-A8FL 
        6.64        30.28 

$`DEL PEAK 38(18Q12.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 
       46.65        23.38        33.53        22.09        22.06         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.08        24.16        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       16.24        24.92         3.02        35.01        58.03        63.98 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3543 
        1.02        13.02         1.02         8.05        29.00         0.99 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       17.95        29.95        20.98         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       47.05        11.01         5.03        26.99        19.04         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        0.99        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       36.03        32.05        53.00        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       26.01        24.00         2.01        25.02        19.07        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N 
       13.94        38.04        30.02        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       27.02         0.99        34.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02R 
        1.02        35.01        35.01        39.06        51.98        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 
       39.98        18.05         0.07        21.37        56.55         0.72 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09         0.95         0.20        21.44        17.82 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-6598 
       50.37        58.39         1.41         5.65        32.94        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 
        6.77       100.01        11.74         3.19         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       37.02        26.04        22.98        16.01        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        14.99        12.99        14.04        12.95 
TCGA-CM-6675 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       13.05        20.42        17.75         7.92        15.12         4.50 
TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       16.14        12.39         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28F 
       10.26       119.70       135.65         7.76        81.37        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6808 
       60.79        98.24        13.64         6.18        35.87        33.67 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       19.43       107.67        74.56        43.07        53.62        51.75 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       26.43        22.09        26.04        13.78        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-WS-AB45 
       52.80         2.79         5.98         5.59        14.76        67.00 

  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE 
                         19.07                          20.07 
[1] "0.1 - 140.4 (19.1)" "0.1 - 135.7 (20.1)"
[1] "hr=" "1"  
D63V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 38(18Q12.2) MUTATED        37        0       15        69         2
  DEL PEAK 38(18Q12.2) WILD-TYPE      35        1       13        62         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(18Q12.2) MUTATED           1        11         11         36
  DEL PEAK 38(18Q12.2) WILD-TYPE         0        10          1         19
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 38(18Q12.2) MUTATED           27       35        14         1
  DEL PEAK 38(18Q12.2) WILD-TYPE         11        8         4         1
D63V3, multiclass
            clus
vv           DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  STAGE I                              37                             35
  STAGE IA                              0                              1
  STAGE II                             15                             13
  STAGE IIA                            69                             62
  STAGE IIB                             2                              6
  STAGE IIC                             1                              0
  STAGE III                            11                             10
  STAGE IIIA                           11                              1
  STAGE IIIB                           36                             19
  STAGE IIIC                           27                             11
  STAGE IV                             35                              8
  STAGE IVA                            14                              4
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 38(18Q12.2) MUTATED     6  44 187  29
  DEL PEAK 38(18Q12.2) WILD-TYPE   5  32 113  22
D63V4, multiclass
    clus
vv   DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  T1                            6                              5
  T2                           44                             32
  T3                          187                            113
  T4                           29                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 38(18Q12.2) MUTATED   136  72  57
  DEL PEAK 38(18Q12.2) WILD-TYPE 120  31  22
D63V5, multiclass
    clus
vv   DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  N0                          136                            120
  N1                           72                             31
  N2                           57                             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                              M0  M1 M1A M1B  MX
  DEL PEAK 38(18Q12.2) MUTATED   186  42   7   1  27
  DEL PEAK 38(18Q12.2) WILD-TYPE 134  10   1   1  23
D63V6, multiclass
     clus
vv    DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  M0                           186                            134
  M1                            42                             10
  M1A                            7                              1
  M1B                            1                              1
  MX                            27                             23
[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"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 38(18Q12.2) MUTATED   119 147
  DEL PEAK 38(18Q12.2) WILD-TYPE  88  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(18Q12.2) MUTATED    119  147
  DEL PEAK 38(18Q12.2) WILD-TYPE   88   85
        clus
vv       DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  FEMALE                          119                             88
  MALE                            147                             85
[1] 2 2
[1] FALSE
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 38(18Q12.2) MUTATED   250  15
  DEL PEAK 38(18Q12.2) WILD-TYPE 128  44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(18Q12.2) MUTATED    250   15
  DEL PEAK 38(18Q12.2) WILD-TYPE  128   44
                               clus
vv                              DEL PEAK 38(18Q12.2) MUTATED
  COLON ADENOCARCINOMA                                   250
  COLON MUCINOUS ADENOCARCINOMA                           15
                               clus
vv                              DEL PEAK 38(18Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     128
  COLON MUCINOUS ADENOCARCINOMA                             44
[1] 2 2
[1] FALSE
D63V9, binary
                                cls
clus                               0   1
  DEL PEAK 38(18Q12.2) MUTATED     3 263
  DEL PEAK 38(18Q12.2) WILD-TYPE   0 173
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 38(18Q12.2) MUTATED      3  263
  DEL PEAK 38(18Q12.2) WILD-TYPE    0  173
     clus
vv    DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  NO                             3                              0
  YES                          263                            173
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 38(18Q12.2) MUTATED   188   1  18  11
  DEL PEAK 38(18Q12.2) WILD-TYPE 125   2   6  14
D63V10, multiclass
    clus
vv   DEL PEAK 38(18Q12.2) MUTATED DEL PEAK 38(18Q12.2) WILD-TYPE
  R0                          188                            125
  R1                            1                              2
  R2                           18                              6
  RX                           11                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(18Q12.2) MUTATED                                  1     6
  DEL PEAK 38(18Q12.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(18Q12.2) MUTATED                          30   132
  DEL PEAK 38(18Q12.2) WILD-TYPE                        20    79
D63V12, multiclass
                                  clus
vv                                 DEL PEAK 38(18Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  30
  WHITE                                                     132
                                  clus
vv                                 DEL PEAK 38(18Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    20
  WHITE                                                        79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = DEL PEAK 39(18Q21.2) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(18Q21.2) MUTATED   217  57
  DEL PEAK 39(18Q21.2) WILD-TYPE 118  30
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                           274                            148 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                            57                             30 
$`DEL PEAK 39(18Q21.2) MUTATED`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 
        5.06         5.26        37.02        43.76        43.43        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       42.28        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 
       37.05        37.25        16.04        34.65        36.53        14.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 
       32.45        32.91        31.63        30.44        29.19        23.61 
TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       22.09        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 
       25.18        20.61        21.76        24.39        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       61.84        52.44         9.63         5.03         1.02         1.02 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 
       37.05         1.02         6.97        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       37.05        36.03        19.07        19.07        34.03        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       26.01        12.99        14.01        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 
       24.00        23.01        19.99        13.94        19.99        61.02 
TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.05        54.02         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02         5.98        37.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 
       85.05        25.02        38.99        36.95        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 
       17.03         0.99        33.07         0.99        31.07        31.07 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 
       17.03        24.03        27.02        29.98        18.05        12.99 
TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 
       50.99        13.05        34.06        26.01        24.00        27.02 
TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U 
        7.96        19.00        34.03        18.05        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        21.99        15.02        15.02         0.99        32.02 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E 
       31.00         1.02        33.04        26.01        37.02         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J 
       39.98         2.01         5.03         0.92        41.00        40.96 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        4.21         0.79         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6386 
        0.43         0.46        14.50        16.31        15.75        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 
        5.19         5.52         6.87        75.25         5.65         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 
       83.80        22.36        65.00        62.79        61.41        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       29.56         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        2.14         3.29         0.07         0.26         1.35       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
       48.20        21.99         2.01         8.02         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 
       13.02        29.06        22.03        30.08         5.03        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 
       17.03        14.04        29.03        16.04        21.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       15.02        11.01        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        14.99        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 
       11.51        20.19        17.75        18.25         1.32        17.85 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49        15.58         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       14.30         9.04        13.41        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
        7.50        44.32       131.51       139.17         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       26.47       119.93        35.97       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 
        8.61        13.38        11.11        13.45         1.55        16.31 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       29.59        16.24        33.67         1.28         0.53        35.41 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       28.21         8.35        82.39        23.51        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 
       44.68        55.04        45.11        39.42        35.93        36.72 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       36.00        26.04        91.79        46.75        47.15         4.11 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 
       10.98        10.52         5.98         1.32         5.19         5.49 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-RU-A8FL 
       26.99        17.29         6.64        30.28 

$`DEL PEAK 39(18Q21.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 
       46.65        23.38        33.53        22.06         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.16        24.69        20.12        19.66        16.24        24.92 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        3.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
        1.02         8.05        29.00         0.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 
       20.98         6.97         0.92        47.05        11.01         5.03 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       26.99        19.04         0.99         0.99        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 
        1.02        17.98        15.95        36.03        32.05        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 
       31.00         2.01        33.01        26.01        24.00         2.01 
TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       25.02        19.07        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       18.05        17.03         4.01        27.02         0.99        34.98 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       12.00        31.00        38.07         1.02        35.01        35.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
       39.06        51.98        22.03        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 
       21.37        56.55         0.72         0.76         0.92        27.09 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        0.95         0.20        21.44        50.37        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5255 TCGA-CA-5796 
       32.94        49.41         6.77       100.01         3.06         3.25 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
        0.33         0.10        17.56        40.34        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       37.02        26.04        22.98        16.01        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        14.99        12.99        14.04        12.95 
TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 
       20.42         7.92        15.12         4.50        16.14        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 TCGA-F4-6570 
      135.65         7.76        81.37        60.79        13.64         6.18 
TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       35.87        19.43       107.67        43.07        53.62        51.75 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       26.43        22.09        13.78        35.80        26.17        52.80 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-WS-AB45 
        2.79         5.59        14.76        67.00 

  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE 
                         19.33                          19.84 
[1] "0.1 - 140.4 (19.3)" "0.1 - 135.7 (19.8)"
[1] "hr=" "1"  
D64V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 39(18Q21.2) MUTATED        39        0       16        71         2
  DEL PEAK 39(18Q21.2) WILD-TYPE      33        1       12        60         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(18Q21.2) MUTATED           1        11         11         39
  DEL PEAK 39(18Q21.2) WILD-TYPE         0        10          1         16
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 39(18Q21.2) MUTATED           30       37        15         2
  DEL PEAK 39(18Q21.2) WILD-TYPE          8        6         3         0
D64V3, multiclass
            clus
vv           DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  STAGE I                              39                             33
  STAGE IA                              0                              1
  STAGE II                             16                             12
  STAGE IIA                            71                             60
  STAGE IIB                             2                              6
  STAGE IIC                             1                              0
  STAGE III                            11                             10
  STAGE IIIA                           11                              1
  STAGE IIIB                           39                             16
  STAGE IIIC                           30                              8
  STAGE IV                             37                              6
  STAGE IVA                            15                              3
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 39(18Q21.2) MUTATED     7  45 195  33
  DEL PEAK 39(18Q21.2) WILD-TYPE   4  31 105  18
D64V4, multiclass
    clus
vv   DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  T1                            7                              4
  T2                           45                             31
  T3                          195                            105
  T4                           33                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 39(18Q21.2) MUTATED   141  76  62
  DEL PEAK 39(18Q21.2) WILD-TYPE 115  27  17
D64V5, multiclass
    clus
vv   DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  N0                          141                            115
  N1                           76                             27
  N2                           62                             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                              M0  M1 M1A M1B  MX
  DEL PEAK 39(18Q21.2) MUTATED   194  45   7   2  30
  DEL PEAK 39(18Q21.2) WILD-TYPE 126   7   1   0  20
D64V6, multiclass
     clus
vv    DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  M0                           194                            126
  M1                            45                              7
  M1A                            7                              1
  M1B                            2                              0
  MX                            30                             20
[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"
D64V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q21.2) MUTATED   123 157
  DEL PEAK 39(18Q21.2) WILD-TYPE  84  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q21.2) MUTATED    123  157
  DEL PEAK 39(18Q21.2) WILD-TYPE   84   75
        clus
vv       DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  FEMALE                          123                             84
  MALE                            157                             75
[1] 2 2
[1] FALSE
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q21.2) MUTATED   262  17
  DEL PEAK 39(18Q21.2) WILD-TYPE 116  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q21.2) MUTATED    262   17
  DEL PEAK 39(18Q21.2) WILD-TYPE  116   42
                               clus
vv                              DEL PEAK 39(18Q21.2) MUTATED
  COLON ADENOCARCINOMA                                   262
  COLON MUCINOUS ADENOCARCINOMA                           17
                               clus
vv                              DEL PEAK 39(18Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     116
  COLON MUCINOUS ADENOCARCINOMA                             42
[1] 2 2
[1] FALSE
D64V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(18Q21.2) MUTATED     3 277
  DEL PEAK 39(18Q21.2) WILD-TYPE   0 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(18Q21.2) MUTATED      3  277
  DEL PEAK 39(18Q21.2) WILD-TYPE    0  159
     clus
vv    DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  NO                             3                              0
  YES                          277                            159
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(18Q21.2) MUTATED   197   1  18  11
  DEL PEAK 39(18Q21.2) WILD-TYPE 116   2   6  14
D64V10, multiclass
    clus
vv   DEL PEAK 39(18Q21.2) MUTATED DEL PEAK 39(18Q21.2) WILD-TYPE
  R0                          197                            116
  R1                            1                              2
  R2                           18                              6
  RX                           11                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(18Q21.2) MUTATED                                  1     6
  DEL PEAK 39(18Q21.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(18Q21.2) MUTATED                          34   141
  DEL PEAK 39(18Q21.2) WILD-TYPE                        16    70
D64V12, multiclass
                                  clus
vv                                 DEL PEAK 39(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  34
  WHITE                                                     141
                                  clus
vv                                 DEL PEAK 39(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                        70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = DEL PEAK 40(19P13.3) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 40(19P13.3) MUTATED    44  15
  DEL PEAK 40(19P13.3) WILD-TYPE 291  72
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                            59                            363 
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                            15                             72 
$`DEL PEAK 40(19P13.3) MUTATED`
TCGA-A6-3807 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3506 TCGA-AA-3519 
       34.65        25.08        21.76        61.84        58.03         9.07 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       26.01        12.99        13.02        23.01        19.99         6.05 
TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3860 TCGA-AA-3866 
        2.01        36.00        36.95        37.02        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 
       24.03        27.02        24.00         2.01        50.99        24.00 
TCGA-AA-A00O TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F 
       27.02         0.99        12.00        33.04        26.01        39.98 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4616 
       41.00         1.02         0.20        16.31         0.20         5.13 
TCGA-AZ-4684 TCGA-CA-5797 TCGA-CK-4948 TCGA-CK-5912 TCGA-CM-6169 TCGA-CM-6675 
       65.00         3.29       102.44        48.20        13.02        13.05 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6541 
       10.06        14.99        20.19         1.32         4.50        15.58 
TCGA-D5-6922 TCGA-DM-A0X9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-F4-6461 TCGA-F4-6808 
       10.13       119.70        44.32       131.51        11.11        33.67 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A50U TCGA-RU-A8FL 
        8.35        82.39        36.00        10.98        30.28 

$`DEL PEAK 40(19P13.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 
       23.38        17.79        42.28        44.91        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 
       13.94        15.52        37.05        37.25        16.04        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       14.53        32.45        32.91        31.63        30.44        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       33.53        23.61        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.18        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        52.44         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        1.02         3.02         1.02        37.05         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       63.98         6.97         1.02        13.02        38.99         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       34.03        29.00        29.00         0.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       21.01        24.00        17.95        29.95        20.98        19.99 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        37.05        19.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
       19.04         0.99         0.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3846 
        1.02        17.98        15.95        38.99        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.99        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       53.00        29.98        18.05        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       21.99        16.08        13.05        34.06        26.01        25.02 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       27.02        19.07         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       19.00        30.02        34.03        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        42.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        15.02        32.02        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02        35.01         1.02        35.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
        4.21        56.55         0.79         0.72         1.58         0.10 
TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.76         0.43         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        15.75        21.44        17.82         5.19         5.52 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        6.87        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       32.94        83.80        22.36        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
        6.77        12.10       100.01        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        3.19         1.94         2.24         3.06         2.14         3.25 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       40.34        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
        2.93         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        8.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       22.03        22.98        30.08        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       12.03        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25         7.92        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       12.49        16.14         7.53        12.39        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41         1.51        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB 
       49.91        13.32        12.59       140.38         7.50       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
        7.76       139.17         6.12        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      119.93        35.97        60.79       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        13.38        13.64        13.45         6.18        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        16.24         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 
       35.41        19.43       107.67        28.21        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       43.07        61.87        53.62        44.68        55.04        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       45.11        39.42        35.93        36.72        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
       26.04        13.78        35.80        26.17        91.79        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       47.15        52.80         4.11        10.52         2.79         5.98 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
        5.59         1.32         5.19         5.49        26.99        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 
        6.64        14.76        67.00 

  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE 
                         23.01                          19.07 
[1] "0.2 - 131.5 (23.0)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.2"
D65V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 40(19P13.3) MUTATED         8        0        1        11         0
  DEL PEAK 40(19P13.3) WILD-TYPE      64        1       27       120         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(19P13.3) MUTATED           0         4          3          5
  DEL PEAK 40(19P13.3) WILD-TYPE         1        17          9         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 40(19P13.3) MUTATED           12       10         4         1
  DEL PEAK 40(19P13.3) WILD-TYPE         26       33        14         1
D65V3, multiclass
            clus
vv           DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  STAGE I                               8                             64
  STAGE IA                              0                              1
  STAGE II                              1                             27
  STAGE IIA                            11                            120
  STAGE IIB                             0                              8
  STAGE IIC                             0                              1
  STAGE III                             4                             17
  STAGE IIIA                            3                              9
  STAGE IIIB                            5                             50
  STAGE IIIC                           12                             26
  STAGE IV                             10                             33
  STAGE IVA                             4                             14
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 40(19P13.3) MUTATED     1   9  43   8
  DEL PEAK 40(19P13.3) WILD-TYPE  10  67 257  43
D65V4, multiclass
    clus
vv   DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  T1                            1                             10
  T2                            9                             67
  T3                           43                            257
  T4                            8                             43
[1] 4 2
[1] 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
  DEL PEAK 40(19P13.3) MUTATED    23  15  23
  DEL PEAK 40(19P13.3) WILD-TYPE 233  88  56
D65V5, multiclass
    clus
vv   DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  N0                           23                            233
  N1                           15                             88
  N2                           23                             56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 40(19P13.3) MUTATED    37  11   3   1   8
  DEL PEAK 40(19P13.3) WILD-TYPE 283  41   5   1  42
D65V6, multiclass
     clus
vv    DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  M0                            37                            283
  M1                            11                             41
  M1A                            3                              5
  M1B                            1                              1
  MX                             8                             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"
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.3) MUTATED    25  36
  DEL PEAK 40(19P13.3) WILD-TYPE 182 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.3) MUTATED     25   36
  DEL PEAK 40(19P13.3) WILD-TYPE  182  196
        clus
vv       DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  FEMALE                           25                            182
  MALE                             36                            196
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.3) MUTATED    55   5
  DEL PEAK 40(19P13.3) WILD-TYPE 323  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.3) MUTATED     55    5
  DEL PEAK 40(19P13.3) WILD-TYPE  323   54
                               clus
vv                              DEL PEAK 40(19P13.3) MUTATED
  COLON ADENOCARCINOMA                                    55
  COLON MUCINOUS ADENOCARCINOMA                            5
                               clus
vv                              DEL PEAK 40(19P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     323
  COLON MUCINOUS ADENOCARCINOMA                             54
[1] 2 2
[1] FALSE
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 40(19P13.3) MUTATED     1  60
  DEL PEAK 40(19P13.3) WILD-TYPE   2 376
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 40(19P13.3) MUTATED      1   60
  DEL PEAK 40(19P13.3) WILD-TYPE    2  376
     clus
vv    DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  NO                             1                              2
  YES                           60                            376
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 40(19P13.3) MUTATED    39   1   7   3
  DEL PEAK 40(19P13.3) WILD-TYPE 274   2  17  22
D65V10, multiclass
    clus
vv   DEL PEAK 40(19P13.3) MUTATED DEL PEAK 40(19P13.3) WILD-TYPE
  R0                           39                            274
  R1                            1                              2
  R2                            7                             17
  RX                            3                             22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(19P13.3) MUTATED                                  0     1
  DEL PEAK 40(19P13.3) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(19P13.3) MUTATED                           6    25
  DEL PEAK 40(19P13.3) WILD-TYPE                        44   186
D65V12, multiclass
                                  clus
vv                                 DEL PEAK 40(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      25
                                  clus
vv                                 DEL PEAK 40(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    44
  WHITE                                                       186
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = DEL PEAK 41(20P12.1) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(20P12.1) MUTATED    67  15
  DEL PEAK 41(20P12.1) WILD-TYPE 268  72
  DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE 
                            82                            340 
  DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE 
                            15                             72 
$`DEL PEAK 41(20P12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       17.79        14.53        29.19        23.61        32.71        29.16 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3519 
       24.13        25.18        21.76         1.02        38.99         9.07 
TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3553 TCGA-AA-3561 
       34.03        26.01        12.99         0.99        24.00        13.94 
TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3855 
       78.08         5.98        85.05        25.02        36.95        32.05 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00F 
       24.03         2.01        20.98         2.01        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01Z TCGA-AA-A02F 
       42.02        32.02        31.00         1.02        37.02        39.98 
TCGA-AA-A03J TCGA-AD-6965 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-5403 TCGA-AZ-6605 
       40.96         0.20        15.75        75.25        62.79         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-5344 
       11.74         1.94       102.44        21.99         2.01        22.03 
TCGA-CM-5349 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       30.08        29.03        12.99        13.02        15.02        11.08 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6929 TCGA-D5-6932 
       13.51        11.51         1.32         7.92        13.41        11.38 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
      119.70        38.20       130.65        92.75        49.91        13.32 
TCGA-DM-A1HA TCGA-DM-A28A TCGA-DM-A28E TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
      131.51        26.47       119.93        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6315 TCGA-G4-6320 
        1.28         0.53         8.35        23.51        36.72        26.43 
TCGA-NH-A50V TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-RU-A8FL 
       10.52         5.49         6.64        30.28 

$`DEL PEAK 41(20P12.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        5.06         5.26        37.02        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       23.38        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       15.52        37.05        37.25        16.04        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       32.45        32.91        31.63        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       22.06        27.09        22.52         8.38        25.08        24.16 
TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        24.69        24.39        23.87        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.28        16.24        24.92        61.84        52.44         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         1.02         3.02         1.02        37.05        35.01 
TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       58.03        63.98         6.97         1.02        13.02         1.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
       24.03        37.05        36.03         8.05        19.07        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        29.00        14.01        33.99        21.01        13.02 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        19.99        19.99 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02         6.05         6.97        54.02         2.01        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        0.92        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00         5.03        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
        0.99         0.99        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
       33.07        36.03         0.99        31.07        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       17.03        27.02        29.98        18.05        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3956 
       12.99        24.00        33.01        26.01        24.00        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       21.99        16.08        50.99        13.05        34.06        26.01 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       25.02        24.00        27.02        19.07         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
       13.94        38.04        30.02        18.05        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
        4.01        27.02         0.99        17.03        14.99        21.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02         0.99        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07        35.01         1.02        33.04        35.01        26.01 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
       22.03        41.00        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
        4.21        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         0.43         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         5.52         6.87        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
        5.65        32.94         5.13        83.80        22.36        65.00 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       61.41        49.41         6.77        12.10       100.01        29.56 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        3.19         2.24         3.06         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        0.07         0.26         0.33         0.10         1.35        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5916 
       40.34        70.16        15.62        48.20        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
        2.93       124.27        23.05        20.02        37.02         8.02 
TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       26.04         8.02        27.02        13.02        29.06        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       16.01        15.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        14.04        16.04        21.99        14.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-6529 
       10.06        12.03        14.99        12.26        19.59        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       20.42        17.75        18.25        15.12        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D8 TCGA-DM-A1D9 
        1.51        12.00        10.26        24.43        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
        7.50        44.32       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       14.04        81.37        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6855 TCGA-F4-6856 
        6.18        35.87         1.55        16.31        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21        82.39        74.56        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 
       53.62        44.68        55.04        51.75        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       35.93        36.00        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       26.17        91.79        46.75        47.15        52.80         4.11 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 
       10.98         2.79         5.98         5.59         1.32         5.19 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-WS-AB45 
       26.99        17.29        14.76        67.00 

  DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE 
                        23.560                         19.055 
[1] "0.2 - 131.5 (23.6)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.3"
D66V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 41(20P12.1) MUTATED        10        0        6        22         0
  DEL PEAK 41(20P12.1) WILD-TYPE      62        1       22       109         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(20P12.1) MUTATED           1         4          2         15
  DEL PEAK 41(20P12.1) WILD-TYPE         0        17         10         40
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 41(20P12.1) MUTATED           10        8         4         0
  DEL PEAK 41(20P12.1) WILD-TYPE         28       35        14         2
D66V3, multiclass
            clus
vv           DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE
  STAGE I                              10                             62
  STAGE IA                              0                              1
  STAGE II                              6                             22
  STAGE IIA                            22                            109
  STAGE IIB                             0                              8
  STAGE IIC                             1                              0
  STAGE III                             4                             17
  STAGE IIIA                            2                             10
  STAGE IIIB                           15                             40
  STAGE IIIC                           10                             28
  STAGE IV                              8                             35
  STAGE IVA                             4                             14
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 41(20P12.1) MUTATED     1  11  62   9
  DEL PEAK 41(20P12.1) WILD-TYPE  10  65 238  42
D66V4, multiclass
    clus
vv   DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE
  T1                            1                             10
  T2                           11                             65
  T3                           62                            238
  T4                            9                             42
[1] 4 2
[1] 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
  DEL PEAK 41(20P12.1) MUTATED    42  23  18
  DEL PEAK 41(20P12.1) WILD-TYPE 214  80  61
D66V5, multiclass
    clus
vv   DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE
  N0                           42                            214
  N1                           23                             80
  N2                           18                             61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 41(20P12.1) MUTATED    62  11   1   0   9
  DEL PEAK 41(20P12.1) WILD-TYPE 258  41   7   2  41
D66V6, multiclass
     clus
vv    DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE
  M0                            62                            258
  M1                            11                             41
  M1A                            1                              7
  M1B                            0                              2
  MX                             9                             41
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(20P12.1) MUTATED    40  43
  DEL PEAK 41(20P12.1) WILD-TYPE 167 189
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(20P12.1) MUTATED     40   43
  DEL PEAK 41(20P12.1) WILD-TYPE  167  189
        clus
vv       DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE
  FEMALE                           40                            167
  MALE                             43                            189
[1] 2 2
[1] FALSE
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(20P12.1) MUTATED    77   6
  DEL PEAK 41(20P12.1) WILD-TYPE 301  53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(20P12.1) MUTATED     77    6
  DEL PEAK 41(20P12.1) WILD-TYPE  301   53
                               clus
vv                              DEL PEAK 41(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                    77
  COLON MUCINOUS ADENOCARCINOMA                            6
                               clus
vv                              DEL PEAK 41(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     301
  COLON MUCINOUS ADENOCARCINOMA                             53
[1] 2 2
[1] FALSE
D66V9, binary
                                cls
clus                               0   1
  DEL PEAK 41(20P12.1) MUTATED     0  83
  DEL PEAK 41(20P12.1) WILD-TYPE   3 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(20P12.1) MUTATED      0   83
  DEL PEAK 41(20P12.1) WILD-TYPE    3  353
     clus
vv    DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE
  NO                             0                              3
  YES                           83                            353
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(20P12.1) MUTATED    55   0   3   2
  DEL PEAK 41(20P12.1) WILD-TYPE 258   3  21  23
D66V10, multiclass
    clus
vv   DEL PEAK 41(20P12.1) MUTATED DEL PEAK 41(20P12.1) WILD-TYPE
  R0                           55                            258
  R1                            0                              3
  R2                            3                             21
  RX                            2                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(20P12.1) MUTATED                                  0     0
  DEL PEAK 41(20P12.1) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(20P12.1) MUTATED                           9    45
  DEL PEAK 41(20P12.1) WILD-TYPE                        41   166
D66V12, multiclass
                                  clus
vv                                 DEL PEAK 41(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      45
                                  clus
vv                                 DEL PEAK 41(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       166
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = DEL PEAK 42(21Q11.2) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(21Q11.2) MUTATED   103  27
  DEL PEAK 42(21Q11.2) WILD-TYPE 232  60
  DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE 
                           130                            292 
  DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE 
                            27                             60 
$`DEL PEAK 42(21Q11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-4105 TCGA-A6-5659 
       37.02        43.76        42.28        37.05        14.53        30.44 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       22.09        22.06        29.16        20.61        21.76        24.39 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       23.87        20.28        61.84         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3538 
       38.99         9.07        19.07        19.07        34.03        26.01 
TCGA-AA-3544 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3685 
       14.01        13.02        23.01        19.99        78.08        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 
       19.00        36.00         0.99        38.99        37.02        14.93 
TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99         0.99        31.07        17.03        24.03        27.02 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 
       18.05        24.00        20.98         2.01        21.99         7.96 
TCGA-AA-A004 TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01C 
       13.94        17.03        27.02        42.02        21.99        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
        0.99        32.02        31.00        51.98        39.98         2.01 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
        0.92        41.00         0.79         1.02         0.20         0.43 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D TCGA-AZ-4616 TCGA-AZ-4684 
       14.50        16.31         0.95         5.52         5.13        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
       12.10        29.56         5.23         3.19         2.24         2.14 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
        3.29         0.26        48.20        21.99         2.01        20.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5862 
        8.02        27.02        13.02        22.03        16.01         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 
       15.02        14.04        29.03        15.02        11.08        11.01 
TCGA-D5-5537 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       14.99        17.75         1.32        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
        9.04        13.41        11.38        49.91        13.32       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
        7.50       131.51        26.47        13.38        35.87         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       29.59        16.24        33.67         0.53        35.41         8.35 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 
       35.93        36.72        36.00        26.43        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A8F7 TCGA-QG-A5YV 
        4.11         5.98         5.19        26.99 

$`DEL PEAK 42(21Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06         5.26        46.65        43.43        23.38        17.79 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        15.52        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       16.04        34.65        36.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       29.19        33.53        23.61        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        24.16        24.69 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3489 
       20.12        19.66        16.24        24.92        52.44         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        3.02         1.02        37.05         1.02        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
       63.98         1.02        13.02         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
       36.03         8.05        29.00        29.00        12.99         0.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       33.99        21.01        24.00        17.95        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       13.94        19.99        61.02         6.05         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 
        2.01        14.01         0.92        50.04        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       15.02        11.01         5.98         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       19.04         0.99        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 
       17.98        15.95        36.95        17.03        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 
       32.05        31.07        53.00        29.98        31.00         2.01 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 
       12.99        33.01        26.01        24.00         2.01        34.03 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       16.08        50.99        13.05        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        27.02        19.07        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       30.02        34.03        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01I 
       17.03        14.99        34.98        15.02        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       38.07         1.02        35.01         1.02        33.04        35.01 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02R 
       26.01        37.02        39.06         2.96         5.03        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       39.98        18.05        40.96         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 
       56.55         0.72         1.58         0.10         0.76         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        15.75         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        5.19         6.87        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
        5.65        32.94        83.80        22.36        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 
       49.41         6.77       100.01        11.74         1.94         3.06 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         0.07         0.33         0.10         1.35        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
      102.44        40.34        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 
        2.93       124.27        23.05        37.02         8.02        26.04 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       29.06        22.98        30.08        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       10.06        12.03        12.26        19.59        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.19        20.42        18.25         7.92        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.50        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       12.39         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 
      119.70        24.43        38.20       130.65        92.75        12.59 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 
       44.32       135.65         7.76       139.17         6.12        14.04 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        13.64        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 
       16.31         1.28        19.43       107.67        28.21        82.39 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6321 TCGA-G4-6322 
       55.04        51.75        45.11        39.42        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50U 
       13.78        35.80        26.17        47.15        52.80        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YX 
       10.52         2.79         5.59         1.32         5.49        17.29 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-WS-AB45 
        6.64        14.76        30.28        67.00 

  DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE 
                        17.900                         20.305 
[1] "0.2 - 140.4 (17.9)" "0.1 - 139.2 (20.3)"
[1] "hr=" "1.2"
D67V2, continuous
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 42(21Q11.2) MUTATED        22        0        8        36         1
  DEL PEAK 42(21Q11.2) WILD-TYPE      50        1       20        95         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(21Q11.2) MUTATED           0         4          5         15
  DEL PEAK 42(21Q11.2) WILD-TYPE         1        17          7         40
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 42(21Q11.2) MUTATED           17       20         4         0
  DEL PEAK 42(21Q11.2) WILD-TYPE         21       23        14         2
D67V3, multiclass
            clus
vv           DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE
  STAGE I                              22                             50
  STAGE IA                              0                              1
  STAGE II                              8                             20
  STAGE IIA                            36                             95
  STAGE IIB                             1                              7
  STAGE IIC                             0                              1
  STAGE III                             4                             17
  STAGE IIIA                            5                              7
  STAGE IIIB                           15                             40
  STAGE IIIC                           17                             21
  STAGE IV                             20                             23
  STAGE IVA                             4                             14
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 42(21Q11.2) MUTATED     6  22  91  17
  DEL PEAK 42(21Q11.2) WILD-TYPE   5  54 209  34
D67V4, multiclass
    clus
vv   DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE
  T1                            6                              5
  T2                           22                             54
  T3                           91                            209
  T4                           17                             34
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 42(21Q11.2) MUTATED    70  32  34
  DEL PEAK 42(21Q11.2) WILD-TYPE 186  71  45
D67V5, multiclass
    clus
vv   DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE
  N0                           70                            186
  N1                           32                             71
  N2                           34                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 42(21Q11.2) MUTATED    91  21   3   0  20
  DEL PEAK 42(21Q11.2) WILD-TYPE 229  31   5   2  30
D67V6, multiclass
     clus
vv    DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE
  M0                            91                            229
  M1                            21                             31
  M1A                            3                              5
  M1B                            0                              2
  MX                            20                             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"
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(21Q11.2) MUTATED    63  73
  DEL PEAK 42(21Q11.2) WILD-TYPE 144 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(21Q11.2) MUTATED     63   73
  DEL PEAK 42(21Q11.2) WILD-TYPE  144  159
        clus
vv       DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE
  FEMALE                           63                            144
  MALE                             73                            159
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(21Q11.2) MUTATED   126   8
  DEL PEAK 42(21Q11.2) WILD-TYPE 252  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(21Q11.2) MUTATED    126    8
  DEL PEAK 42(21Q11.2) WILD-TYPE  252   51
                               clus
vv                              DEL PEAK 42(21Q11.2) MUTATED
  COLON ADENOCARCINOMA                                   126
  COLON MUCINOUS ADENOCARCINOMA                            8
                               clus
vv                              DEL PEAK 42(21Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     252
  COLON MUCINOUS ADENOCARCINOMA                             51
[1] 2 2
[1] FALSE
D67V9, binary
                                cls
clus                               0   1
  DEL PEAK 42(21Q11.2) MUTATED     2 134
  DEL PEAK 42(21Q11.2) WILD-TYPE   1 302
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(21Q11.2) MUTATED      2  134
  DEL PEAK 42(21Q11.2) WILD-TYPE    1  302
     clus
vv    DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE
  NO                             2                              1
  YES                          134                            302
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(21Q11.2) MUTATED    93   1  10   7
  DEL PEAK 42(21Q11.2) WILD-TYPE 220   2  14  18
D67V10, multiclass
    clus
vv   DEL PEAK 42(21Q11.2) MUTATED DEL PEAK 42(21Q11.2) WILD-TYPE
  R0                           93                            220
  R1                            1                              2
  R2                           10                             14
  RX                            7                             18
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(21Q11.2) MUTATED                                  1     4
  DEL PEAK 42(21Q11.2) WILD-TYPE                                0     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(21Q11.2) MUTATED                          14    66
  DEL PEAK 42(21Q11.2) WILD-TYPE                        36   145
D67V12, multiclass
                                  clus
vv                                 DEL PEAK 42(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                      66
                                  clus
vv                                 DEL PEAK 42(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    36
  WHITE                                                       145
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = DEL PEAK 43(22Q13.32) MUTATION ANALYSIS
D68V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 43(22Q13.32) MUTATED   115  35
  DEL PEAK 43(22Q13.32) WILD-TYPE 220  52
  DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE 
                            150                             272 
  DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE 
                             35                              52 
$`DEL PEAK 43(22Q13.32) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
       37.02        42.28        44.91        35.11        45.60        13.94 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5659 
       15.52        34.65        36.53        14.53        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 
       29.19        23.61        22.52        20.61        21.76        23.87 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
       61.84        52.44         9.63         6.97        38.99         9.07 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
       24.03        37.05        29.00        26.01        12.99        33.99 
TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3662 TCGA-AA-3666 
       21.01        13.02        19.99        13.94         6.05         2.01 
TCGA-AA-3673 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3837 
       50.04         5.98        37.05        85.05         0.99        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       36.95        37.02        17.03         0.99        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3869 
        0.99        31.07        31.07        17.03        24.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 
       29.98        18.05         2.01        12.99         2.01         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A004 
       21.99        50.99        13.05        26.01         7.96        13.94 
TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z 
       34.03        27.02        42.02        17.03        14.99        21.99 
TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02W 
       15.02        33.04        26.01        37.02        39.98        41.00 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
       40.96         1.58         1.02         0.20         0.43        14.50 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4323 TCGA-AZ-4614 
       16.31        15.75         0.20         5.52         1.41         5.65 
TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 
        5.13        12.10        29.56         5.23         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-6748 
        2.24         3.06         0.26         1.35        48.20         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
        8.02         8.02        29.06        30.08         5.03        15.02 
TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 
       15.02        11.08        11.01        10.06        14.99        13.51 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       20.19         1.32         7.92        15.12        17.85        12.49 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D7 
        7.53        12.43        13.41        11.38       130.65        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A 
       12.59       140.38        44.32       131.51         6.12        26.47 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6297 
       13.38         1.55        16.24         1.28         8.35        82.39 
TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       51.75        45.11        36.72        36.00        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL 
        4.11        10.98        10.52         5.98        26.99        30.28 

$`DEL PEAK 43(22Q13.32) WILD-TYPE`
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        5.06         5.26        46.65        43.76        43.43        23.38 
TCGA-A6-2677 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 
       17.79        37.05        37.25        16.04        32.45        32.91 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        24.16        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 
        5.03         1.02         3.02         1.02        37.05         1.02 
TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         1.02        13.02         1.02 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 
       36.03         8.05        19.07        19.07        34.03        29.00 
TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
        0.99        14.01        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        19.99        61.02        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01         0.92        47.05        47.01        15.02        11.01 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00        36.00         5.03        26.99        19.04         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       14.93        36.03        53.00        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 
       26.01        24.00        20.98        34.03        16.08        34.06 
TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       25.02        24.00        27.02        19.07        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       19.00        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
        0.99        34.98        15.02         0.99        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       35.01        39.06        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
        0.92        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 
        4.21        56.55         0.79         0.72         0.10         0.76 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.46         0.92        27.09         0.95        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 
        5.19         6.87        75.25        50.37        58.39        32.94 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
       83.80        22.36        65.00        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        6.77       100.01        11.74         2.14         3.25         3.29 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.33         0.10        17.56       102.44        40.34 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        20.02        37.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       13.02        22.03        22.98        16.01        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
       17.03        15.02        12.00        14.04        29.03        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       12.95        13.05        11.08        12.03        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 
       11.51        20.42        17.75        18.25         4.50        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 
       16.14        15.58        12.39        10.13        14.30         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64         1.51        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB 
       24.43        38.20        92.75        49.91         7.50       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
        7.76       139.17        14.04        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
       60.79       117.07        98.24        95.18         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       13.64        13.45         6.18        35.87        16.31        29.59 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67         0.53        35.41        19.43       107.67        28.21 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       23.51        74.56        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 
       55.04        39.42        35.93        26.43        22.09        26.04 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A5IV 
       13.78        35.80        26.17        47.15        52.80         2.79 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F7 TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 
        5.59         1.32         5.19         5.49        17.29         6.64 
TCGA-QG-A5Z2 TCGA-WS-AB45 
       14.76        67.00 

  DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE 
                           0.20                            0.07 
  DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE 
                          16.67                           20.35 
[1] "0.2 - 140.4 (16.7)" "0.1 - 139.2 (20.4)"
[1] "hr=" "1.4"
D68V2, continuous
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 43(22Q13.32) MUTATED        18        0        7        39         1
  DEL PEAK 43(22Q13.32) WILD-TYPE      54        1       21        92         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(22Q13.32) MUTATED           0         7          7         18
  DEL PEAK 43(22Q13.32) WILD-TYPE         1        14          5         37
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 43(22Q13.32) MUTATED           20       24         8         0
  DEL PEAK 43(22Q13.32) WILD-TYPE         18       19        10         2
D68V3, multiclass
            clus
vv           DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE
  STAGE I                               18                              54
  STAGE IA                               0                               1
  STAGE II                               7                              21
  STAGE IIA                             39                              92
  STAGE IIB                              1                               7
  STAGE IIC                              0                               1
  STAGE III                              7                              14
  STAGE IIIA                             7                               5
  STAGE IIIB                            18                              37
  STAGE IIIC                            20                              18
  STAGE IV                              24                              19
  STAGE IVA                              8                              10
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 43(22Q13.32) MUTATED     3  23 106  21
  DEL PEAK 43(22Q13.32) WILD-TYPE   8  53 194  30
D68V4, multiclass
    clus
vv   DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE
  T1                             3                               8
  T2                            23                              53
  T3                           106                             194
  T4                            21                              30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 43(22Q13.32) MUTATED    71  44  38
  DEL PEAK 43(22Q13.32) WILD-TYPE 185  59  41
D68V5, multiclass
    clus
vv   DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE
  N0                            71                             185
  N1                            44                              59
  N2                            38                              41
[1] 3 2
[1] 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 M1A M1B  MX
  DEL PEAK 43(22Q13.32) MUTATED   102  28   4   0  16
  DEL PEAK 43(22Q13.32) WILD-TYPE 218  24   4   2  34
D68V6, multiclass
     clus
vv    DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE
  M0                            102                             218
  M1                             28                              24
  M1A                             4                               4
  M1B                             0                               2
  MX                             16                              34
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                                 cls
clus                                0   1
  DEL PEAK 43(22Q13.32) MUTATED    70  83
  DEL PEAK 43(22Q13.32) WILD-TYPE 137 149
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(22Q13.32) MUTATED     70   83
  DEL PEAK 43(22Q13.32) WILD-TYPE  137  149
        clus
vv       DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE
  FEMALE                            70                             137
  MALE                              83                             149
[1] 2 2
[1] FALSE
D68V8, binary
                                 cls
clus                                0   1
  DEL PEAK 43(22Q13.32) MUTATED   143  10
  DEL PEAK 43(22Q13.32) WILD-TYPE 235  49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(22Q13.32) MUTATED    143   10
  DEL PEAK 43(22Q13.32) WILD-TYPE  235   49
                               clus
vv                              DEL PEAK 43(22Q13.32) MUTATED
  COLON ADENOCARCINOMA                                    143
  COLON MUCINOUS ADENOCARCINOMA                            10
                               clus
vv                              DEL PEAK 43(22Q13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                      235
  COLON MUCINOUS ADENOCARCINOMA                              49
[1] 2 2
[1] FALSE
D68V9, binary
                                 cls
clus                                0   1
  DEL PEAK 43(22Q13.32) MUTATED     1 152
  DEL PEAK 43(22Q13.32) WILD-TYPE   2 284
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 43(22Q13.32) MUTATED      1  152
  DEL PEAK 43(22Q13.32) WILD-TYPE    2  284
     clus
vv    DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE
  NO                              1                               2
  YES                           152                             284
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 43(22Q13.32) MUTATED   103   1  10  11
  DEL PEAK 43(22Q13.32) WILD-TYPE 210   2  14  14
D68V10, multiclass
    clus
vv   DEL PEAK 43(22Q13.32) MUTATED DEL PEAK 43(22Q13.32) WILD-TYPE
  R0                           103                             210
  R1                             1                               2
  R2                            10                              14
  RX                            11                              14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(22Q13.32) MUTATED                                  1     4
  DEL PEAK 43(22Q13.32) WILD-TYPE                                0     7
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(22Q13.32) MUTATED                          19    69
  DEL PEAK 43(22Q13.32) WILD-TYPE                        31   142
D68V12, multiclass
                                  clus
vv                                 DEL PEAK 43(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                       69
                                  clus
vv                                 DEL PEAK 43(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          7
  BLACK OR AFRICAN AMERICAN                                     31
  WHITE                                                        142
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
