[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"            "-oTCOADREAD-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/COADREAD-TP/10005910/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/10013759/transformed.cor.cli.txt"

nPatients in clinical file=612, in cluster file=600, common to both=592
[1]  75 592
[1] "AMP PEAK  1(1Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          141                           451 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          141                           451 
[1] "AMP PEAK  2(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          131                           461 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          131                           461 
[1] "AMP PEAK  3(5P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        110                         482 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        110                         482 
[1] "AMP PEAK  4(5Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           63                           529 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           63                           529 
[1] "AMP PEAK  5(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          148                           444 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          148                           444 
[1] "AMP PEAK  6(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           203                            389 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           203                            389 
[1] "AMP PEAK  7(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           246                            346 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           246                            346 
[1] "AMP PEAK  8(8Q12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                          318                           274 
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                          318                           274 
[1] "AMP PEAK  9(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           353                            239 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           353                            239 
[1] "AMP PEAK 10(10Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE 
                            36                            556 
  AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE 
                            36                            556 
[1] "AMP PEAK 11(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE 
                           132                            460 
  AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE 
                           132                            460 
[1] "AMP PEAK 12(12P13.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE 
                            146                             446 
  AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE 
                            146                             446 
[1] "AMP PEAK 13(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            384                             208 
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            384                             208 
[1] "AMP PEAK 14(13Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           379                            213 
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           379                            213 
[1] "AMP PEAK 15(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           382                            210 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           382                            210 
[1] "AMP PEAK 16(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            42                            550 
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            42                            550 
[1] "AMP PEAK 17(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                           165                            427 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                           165                            427 
[1] "AMP PEAK 18(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                         150                          442 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                         150                          442 
[1] "AMP PEAK 19(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                           135                            457 
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                           135                            457 
[1] "AMP PEAK 20(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                           104                            488 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                           104                            488 
[1] "AMP PEAK 21(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                         131                          461 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                         131                          461 
[1] "AMP PEAK 22(20P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE 
                            311                             281 
  AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE 
                            311                             281 
[1] "AMP PEAK 23(20P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE 
                            349                             243 
  AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE 
                            349                             243 
[1] "AMP PEAK 24(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                            450                             142 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                            450                             142 
[1] "AMP PEAK 25(20Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE 
                         452                          140 
  AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE 
                         452                          140 
[1] "AMP PEAK 26(20Q13.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE 
                            455                             137 
  AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE 
                            455                             137 
[1] "AMP PEAK 27(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                        120                         472 
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                        120                         472 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           234                            358 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           234                            358 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        167                         425 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        167                         425 
[1] "DEL PEAK  3(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          167                           425 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          167                           425 
[1] "DEL PEAK  4(2P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         571 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         571 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           34                           558 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           34                           558 
[1] "DEL PEAK  6(2Q37.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           31                           561 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           31                           561 
[1] "DEL PEAK  7(3P26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE 
                           89                           503 
  DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE 
                           89                           503 
[1] "DEL PEAK  8(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          110                           482 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          110                           482 
[1] "DEL PEAK  9(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            60                            532 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            60                            532 
[1] "DEL PEAK 10(4P16.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE 
                          190                           402 
  DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE 
                          190                           402 
[1] "DEL PEAK 11(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          210                           382 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          210                           382 
[1] "DEL PEAK 12(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          219                           373 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          219                           373 
[1] "DEL PEAK 13(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                          147                           445 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                          147                           445 
[1] "DEL PEAK 14(5Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          178                           414 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          178                           414 
[1] "DEL PEAK 15(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           78                           514 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           78                           514 
[1] "DEL PEAK 16(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         90                         502 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         90                         502 
[1] "DEL PEAK 17(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           16                           576 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           16                           576 
[1] "DEL PEAK 18(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          278                           314 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          278                           314 
[1] "DEL PEAK 19(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        292                         300 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        292                         300 
[1] "DEL PEAK 20(8P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE 
                           128                            464 
  DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE 
                           128                            464 
[1] "DEL PEAK 21(8Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           46                           546 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           46                           546 
[1] "DEL PEAK 22(9P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE 
                           81                           511 
  DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE 
                           81                           511 
[1] "DEL PEAK 23(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           126                            466 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           126                            466 
[1] "DEL PEAK 24(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            153                             439 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            153                             439 
[1] "DEL PEAK 25(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           150                            442 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           150                            442 
[1] "DEL PEAK 26(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           109                            483 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           109                            483 
[1] "DEL PEAK 27(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            86                            506 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            86                            506 
[1] "DEL PEAK 28(12Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             85                             507 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             85                             507 
[1] "DEL PEAK 29(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           200                            392 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           200                            392 
[1] "DEL PEAK 30(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           207                            385 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           207                            385 
[1] "DEL PEAK 31(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                           208                            384 
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                           208                            384 
[1] "DEL PEAK 32(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                           240                            352 
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                           240                            352 
[1] "DEL PEAK 33(15Q15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                           237                            355 
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                           237                            355 
[1] "DEL PEAK 34(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                           235                            357 
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                           235                            357 
[1] "DEL PEAK 35(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                            225                             367 
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                            225                             367 
[1] "DEL PEAK 36(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            65                            527 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            65                            527 
[1] "DEL PEAK 37(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            79                            513 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            79                            513 
[1] "DEL PEAK 38(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                         353                          239 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                         353                          239 
[1] "DEL PEAK 39(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                            89                            503 
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                            89                            503 
[1] "DEL PEAK 40(18P11.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                            352                             240 
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                            352                             240 
[1] "DEL PEAK 41(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           396                            196 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           396                            196 
[1] "DEL PEAK 42(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           414                            178 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           414                            178 
[1] "DEL PEAK 43(18Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                           409                            183 
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                           409                            183 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            93                            499 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            93                            499 
[1] "DEL PEAK 45(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                           181                            411 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                           181                            411 
[1] "DEL PEAK 46(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                           181                            411 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                           181                            411 
[1] "DEL PEAK 47(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                           206                            386 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                           206                            386 
[1] "DEL PEAK 48(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            218                             374 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            218                             374 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "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 592 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
         154         1126         1419         1331         1321          711 
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 
         541         1286         1366         1068         1387           NA 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
         472         1127         1133          488         1054         1111 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
          NA          987         1001          962          926          888 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
        1020          718          672          671          995          887 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
         824          685          734          255          763          766 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
         735          627          662          751          742          726 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
         612          598          617           NA           NA           NA 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
        1595          293           NA           31           NA           31 
TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3511 
        1127           31         1065         1765         1946          212 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 
          31           NA         1186           31          276          731 
TCGA-AA-3521 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3527 
          NA         1127         1096          245          580           NA 
TCGA-AA-3529 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
          NA          580         1035          882          882          791 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
         395           30          426         1034          639           NA 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 
         730          546          911          700          638          608 
TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
         424          608         1856         2375          184          212 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        1643           NA          426           28         1522         1431 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3684 TCGA-AA-3685 
        1430          457           NA          182           NA         1127 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3693 TCGA-AA-3695 TCGA-AA-3696 TCGA-AA-3697 
         578           NA           NA           NA           NA         2587 
TCGA-AA-3710 TCGA-AA-3712 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
         821           NA          579           30           30         1066 
TCGA-AA-3814 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
          NA           NA          761           31          547          485 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3845 TCGA-AA-3846 
        1186         1124         1126          454           NA          518 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
          30           NA         1006           NA         1096          975 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 
          30          945          945         1612          518          731 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3872 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
          NA          912           NA          549          943           NA 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
         395          730         1004          791          730           NA 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
         638         1035           61          669          489         1551 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
         397         1036          791          761          730          822 
TCGA-AA-3984 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
          NA          580           NA          822          424         1157 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L 
         578          913         1035          549          549          518 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
          NA          822         1278           30          518          456 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
         669         1064          457          457           30          974 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
         365          943          943           NA           31         1065 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A022 
          31         1005         1065          791         1126           NA 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
          NA         1581           NA         1216           NA           NA 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
          28           NA         1247         1216           NA         1246 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
           2          650          128         1720           24           22 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EJ 
          48           31            3           23            6           NA 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
          13           14           28          441          824           NA 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
          NA          479            6          652          542          158 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
         168         2289         1532         1776           NA           NA 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1002           NA         2549           NA         1977           NA 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
        1868           NA           NA           NA           NA           NA 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
          NA           NA           NA           NA           68           93 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
          65           99          100            2            8           10 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
           3           41          534         3116         1227         2134 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5915 TCGA-CK-5916 
         475         1466         1561          669           NA           NA 
TCGA-CK-6746 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
          NA           89           61         3780          701          609 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
        1126          244          792          244          822          396 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
         884          670          699          915          487          457 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
          NA          457          457          518          457          365 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
         427          883          488          669          456          395 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
         396          457          427          335          394          397 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
         337          337          335          306          366          456 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
         373          596          411          350          614          621 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
         540          555           40          241          460          543 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
         137          521          380          491          474          229 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
         377          308          378          435          275          287 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
         354          408           46          365          346          312 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
        3641          743         1162         3974         2821         1518 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
         405          383         4270          228         1348         4000 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A 
        4126          236         4233          186          427          805 
TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
        2475         3648         1094         1849         3561         2988 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
        2895           NA          407           NA          415          409 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
          NA         1091           47          496          900          494 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
        1024           39           16         1077          591         3275 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
          NA          254         2506           NA         2268         1310 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
        1882         1631         1359         1674         1574         1372 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
        1199         1093         1117         1095          804          672 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 
         792          419         1089          796         2792           NA 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
        1434         1606          125          154           85          182 
TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 
         170          821          526          449          734          546 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
         524         1309          412          581          387         1148 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
          NA          441          257          468          609          316 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
          NA          365          974          244          215           31 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
          61           NA           31         1400           NA           NA 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3601 
        1035           NA         1522          366          184           NA 
TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
          NA           30          485          608           NA          608 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
          NA          243           30          912           31         1003 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
          30           30           NA          608           31           NA 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1124          518          396         1065          426           31 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1461           NA          974          608          853         1096 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 TCGA-AG-4021 TCGA-AG-4022 
         427           31          518           NA           NA           30 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
         638          424          183          790          700         1126 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
         485         1096          276           31          365          943 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
        2130         1947          334           NA         1520           NA 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
          NA         1885         1247         1157           15           44 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
          21           22          140           55          310          184 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
         184           NA          212          285          144          425 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        1826          243          334          335          457          395 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
         365          425          457         1095          216          914 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
         394          397          306          161         3846         1258 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
        1741         3932          734         1566          992           15 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
          73          625          607          636          517          556 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
         482          538          497          496          499          262 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
         350          328          415          531          364          257 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
          NA         1141          952          452           12           31 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
          20           21           16           34           23           14 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
          NA         1696           NA          804 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=95,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=335,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	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=27,	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=29,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "PRIMARY.SITE.OF.DISEASE"               
 [3] "NEOPLASM.DISEASESTAGE"                 
 [4] "PATHOLOGY.T.STAGE"                     
 [5] "PATHOLOGY.N.STAGE"                     
 [6] "PATHOLOGY.M.STAGE"                     
 [7] "GENDER"                                
 [8] "HISTOLOGICAL.TYPE"                     
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "COMPLETENESS.OF.RESECTION"             
[11] "NUMBER.OF.LYMPH.NODES"                 
[12] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 592 columns, 1 survival variables, and 12 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=2, binary=FALSE, numeric=FALSE
NEOPLASM.DISEASESTAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  19 105 403  62 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   20   105   403    62 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  19 105 403  62 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   20   105   403    62 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
335 146 108 
[1] "table(vv)"
vv
 N0  N1  N2 
335 146 108 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2 
335 146 108 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
335 146 108 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=27, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q31.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1Q31.1) MUTATED   105  30
  AMP PEAK  1(1Q31.1) WILD-TYPE 352  76
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          135                           428 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                           30                            76 
$`AMP PEAK  1(1Q31.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2683 
       37.02        43.76        44.91        35.11        45.60        15.52 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 
       36.53        32.45        29.19        24.16        24.69        23.87 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 
       52.44         5.03        38.99        13.94        78.08        54.02 
TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3688 TCGA-AA-3696 
        2.01        47.05        47.01        15.02        19.00         5.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
        0.99        33.07        32.05        31.07        17.03        27.02 
TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3994 TCGA-AA-A01D 
       12.99        33.01        21.99        13.05        27.02         0.99 
TCGA-AA-A01F TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02Y TCGA-AD-6888 
       32.02        35.01        26.01         2.96        39.98         4.21 
TCGA-AD-6901 TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4682 
        1.02        14.50         0.20         5.52         5.65        22.36 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 
       65.00        12.10        11.74         2.24         3.06         0.26 
TCGA-CK-5912 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       48.20        37.02         8.02        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6167 TCGA-D5-5539 TCGA-D5-6533 
        5.03        15.02        14.04        14.99        19.59         1.32 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       15.12        17.85        12.49         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28K 
       14.30       119.70        92.75        81.37        35.97        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6855 TCGA-G4-6297 
       95.18         8.61        13.38        11.11        35.41        82.39 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6311 TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV 
       74.56        61.87        39.42         4.11         5.98        26.99 
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 
       24.13        13.55        14.50        15.39        10.39        32.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3999 
       46.03        34.03         6.05        19.99        19.99        28.04 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A023 
       23.01        37.02        36.03        31.00        70.03        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        38.96        38.04         0.49         0.69         0.72 
TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 
       10.19         9.37         4.73        11.01        13.97        15.02 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6882 TCGA-EI-6884 
      129.27        24.13        32.61        20.55         8.61        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 
       13.64        11.97         9.96         0.39         0.69         0.76 
TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
       18.28        47.08        26.43 

$`AMP PEAK  1(1Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 
       13.94        37.05        37.25        16.04        34.65        14.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        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-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        21.76        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-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-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-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 
       19.99        61.02         6.05         6.97        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3697 
       50.04        11.01         5.98        37.05        36.00        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-3854 TCGA-AA-3856 TCGA-AA-3860 
       37.02        14.93        17.03        36.03         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        24.03        29.98        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       24.00        26.01        24.00         2.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
        2.01        16.08        50.99        34.06        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02        19.07         7.96        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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I 
       21.99        34.98        15.02        15.02        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-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        39.06        51.98        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        41.00        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6963 
       21.37        56.55         0.79         0.72         1.58         0.10 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.76         0.20         0.43         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-4615 TCGA-AZ-4616 
       75.25        50.37        58.39         1.41        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       83.80        62.79        61.41        49.41         6.77       100.01 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-5796 
       29.56         5.23         3.19         1.94         2.14         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         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-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 
       21.01         2.93         2.01       124.27        23.05        20.02 
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-5860 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       16.01        15.02        17.03        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        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-D5-5540 TCGA-D5-5541 
       10.06        12.03        14.99        12.26        13.51        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-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 
       17.13        16.14        15.58        12.39         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-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43        38.20       130.65        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-A28E TCGA-DM-A28G 
      139.17         6.12        14.04        26.47       119.93        60.79 
TCGA-DM-A28H TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
      117.07        13.64        13.45         6.18        35.87         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-F4-6856 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-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6314 
       53.62        44.68        55.04        51.75        45.11        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-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 
        5.06         2.79         5.59        17.29        14.76        17.95 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.23        43.04        19.10        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
        8.45        20.02        36.03        12.00         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
        1.02         2.01        24.00         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
       29.98         1.02        32.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 
       15.95         9.07         1.02        12.00        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       49.97        61.97        41.00         1.45         4.60         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.05         6.97        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       10.98        15.02        12.99        12.00        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       41.36        57.24        51.48         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 
       16.31        16.41        11.51        17.46         8.45        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       31.30        14.86         1.02         0.66         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6235 
        0.46        55.76 

  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                         0.20                          0.07 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                       129.27                        140.38 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                        19.59                         17.77 
[1] "0.2 - 129.3 (19.6)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D1V2, continuous
D1V3, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED    92  47
  AMP PEAK  1(1Q31.1) WILD-TYPE 337 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     92   47
  AMP PEAK  1(1Q31.1) WILD-TYPE  337  112
        clus
vv       AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  COLON                           92                           337
  RECTUM                          47                           112
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  1(1Q31.1) MUTATED        17        0        7        34         2
  AMP PEAK  1(1Q31.1) WILD-TYPE      85        1       29       131         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1Q31.1) MUTATED           1         6          7         17
  AMP PEAK  1(1Q31.1) WILD-TYPE         2        20         15         59
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  1(1Q31.1) MUTATED           17       21         8         0
  AMP PEAK  1(1Q31.1) WILD-TYPE         35       39        17         1
D1V4, multiclass
            clus
vv           AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  STAGE I                             17                            85
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           34                           131
  STAGE IIB                            2                             8
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           7                            15
  STAGE IIIB                          17                            59
  STAGE IIIC                          17                            35
  STAGE IV                            21                            39
  STAGE IVA                            8                            17
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  AMP PEAK  1(1Q31.1) MUTATED       4  21  94  21
  AMP PEAK  1(1Q31.1) WILD-TYPE    16  84 309  41
D1V5, multiclass
       clus
vv      AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  T0+T1                           4                            16
  T2                             21                            84
  T3                             94                           309
  T4                             21                            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
  AMP PEAK  1(1Q31.1) MUTATED    67  38  33
  AMP PEAK  1(1Q31.1) WILD-TYPE 268 108  75
D1V6, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  N0                          67                           268
  N1                          38                           108
  N2                          33                            75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  1(1Q31.1) MUTATED    96  25   3   0  13
  AMP PEAK  1(1Q31.1) WILD-TYPE 347  47   6   1  45
D1V7, multiclass
     clus
vv    AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  M0                           96                           347
  M1                           25                            47
  M1A                           3                             6
  M1B                           0                             1
  MX                           13                            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"
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED    59  82
  AMP PEAK  1(1Q31.1) WILD-TYPE 218 233
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     59   82
  AMP PEAK  1(1Q31.1) WILD-TYPE  218  233
        clus
vv       AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  FEMALE                          59                           218
  MALE                            82                           233
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                     84
  AMP PEAK  1(1Q31.1) WILD-TYPE                  289
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                               8
  AMP PEAK  1(1Q31.1) WILD-TYPE                            47
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                      43
  AMP PEAK  1(1Q31.1) WILD-TYPE                   100
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                                3
  AMP PEAK  1(1Q31.1) WILD-TYPE                             10
D1V9, multiclass
                                clus
vv                               AMP PEAK  1(1Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    84
  COLON MUCINOUS ADENOCARCINOMA                            8
  RECTAL ADENOCARCINOMA                                   43
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               AMP PEAK  1(1Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     289
  COLON MUCINOUS ADENOCARCINOMA                             47
  RECTAL ADENOCARCINOMA                                    100
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED     5 136
  AMP PEAK  1(1Q31.1) WILD-TYPE   4 447
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED      5  136
  AMP PEAK  1(1Q31.1) WILD-TYPE    4  447
     clus
vv    AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  NO                            5                             4
  YES                         136                           447
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1Q31.1) MUTATED    97   1  11   6
  AMP PEAK  1(1Q31.1) WILD-TYPE 329   4  25  21
D1V11, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  R0                          97                           329
  R1                           1                             4
  R2                          11                            25
  RX                           6                            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"
D1V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  1(1Q31.1) MUTATED                                  0     3
  AMP PEAK  1(1Q31.1) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q31.1) MUTATED                          11    78
  AMP PEAK  1(1Q31.1) WILD-TYPE                        33   214
D1V13, multiclass
                                  clus
vv                                 AMP PEAK  1(1Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     78
                                  clus
vv                                 AMP PEAK  1(1Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   33
  WHITE                                                      214
[1] 4 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(2Q33.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(2Q33.1) MUTATED    96  27
  AMP PEAK  2(2Q33.1) WILD-TYPE 361  79
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          123                           440 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                           27                            79 
$`AMP PEAK  2(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-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4950 TCGA-CK-5914 
        5.13         3.19         0.07         0.26        40.34        21.99 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
        8.02        29.06         5.03        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-D5-5537 TCGA-D5-5541 TCGA-D5-6537 
       29.03        21.99        14.99        14.99        11.51         4.50 
TCGA-D5-6538 TCGA-D5-6898 TCGA-DM-A0XD TCGA-DM-A1DA TCGA-DM-A280 TCGA-DM-A288 
       17.13         7.53        24.43         7.50         7.76        14.04 
TCGA-DM-A28A TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6704 TCGA-G4-6295 TCGA-G4-6299 
       26.47        35.97         8.61         1.55         8.35        74.56 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-QG-A5YX 
       45.11        39.42        47.15        52.80         4.11        17.29 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       24.13        17.95        17.23        10.39         8.45        15.39 
TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3883 
       36.03        46.03         6.05        19.99        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 
       17.03         1.02        48.03        28.04         1.02         0.99 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       12.00        31.00        70.03        38.04         0.49         0.69 
TCGA-AH-6897 TCGA-BM-6198 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
        4.60        10.19        13.97        60.03         7.99        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EF-5831 
       12.00        15.02        36.00        13.05       129.27         2.40 
TCGA-EI-6508 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6863 
       20.91        16.31        13.64         9.96        37.51         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        0.46        18.28        47.08 

$`AMP PEAK  2(2Q33.1) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       37.25        16.04        32.45        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       23.61        22.09        22.06        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        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-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-3538 TCGA-AA-3542 TCGA-AA-3543 
        8.05        19.07        19.07        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-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-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 
        0.92        47.05        47.01        11.01         5.98        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 
       36.00        85.05        26.99        19.04         0.99         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-3854 TCGA-AA-3855 
       37.02        14.93        17.03         0.99        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        31.07        31.07        53.00        17.03        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        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-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
        2.01        21.99        50.99        13.05        34.06        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-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-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98        15.02        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01K 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-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        37.02        39.06        51.98        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-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 
       40.96         0.07        56.55         0.79         0.72         0.76 
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-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-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-6608 TCGA-CA-5254 
      100.01        29.56         5.23        11.74         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 
        3.06         2.14         3.25         3.29         0.33         0.10 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
        1.35        17.56       102.44        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.01         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-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-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       15.02        12.00        16.04        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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        12.26        19.59        13.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       15.12        17.85        12.49        16.14        15.58        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-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         1.51        12.00        11.38        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-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A285 
      140.38        44.32       131.51       135.65       139.17         6.12 
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-F4-6460 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-G4-6297 TCGA-G4-6298 
       35.41        19.43       107.67        28.21        82.39        23.51 
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-G4-6314 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-NH-A50V 
       13.78        35.80        26.17        91.79        46.75         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-AF-2691 
        2.79         5.98         5.59        26.99        14.76        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6655 
       13.55        19.10        12.72        37.74        14.50        20.02 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       10.39        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
       29.98         1.02        32.98         0.99         0.99        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 
       13.02        35.01        14.01        32.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 
       61.97        41.00         1.45         0.72         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-4749 
        6.05         6.97         9.37         4.73        10.98        11.01 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        13.97         7.10        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 
       10.78        17.46        11.97         8.45        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                       129.27                        140.38 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                       16.310                        18.265 
[1] "0.1 - 129.3 (16.3)" "0.1 - 140.4 (18.3)"
[1] "hr=" "1.6"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    84  47
  AMP PEAK  2(2Q33.1) WILD-TYPE 345 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     84   47
  AMP PEAK  2(2Q33.1) WILD-TYPE  345  112
        clus
vv       AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  COLON                           84                           345
  RECTUM                          47                           112
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  2(2Q33.1) MUTATED        21        0        8        25         0
  AMP PEAK  2(2Q33.1) WILD-TYPE      81        1       28       140        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(2Q33.1) MUTATED           2         6          5         20
  AMP PEAK  2(2Q33.1) WILD-TYPE         1        20         17         56
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(2Q33.1) MUTATED           20       14         5         0
  AMP PEAK  2(2Q33.1) WILD-TYPE         32       46        20         1
D2V4, multiclass
            clus
vv           AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  STAGE I                             21                            81
  STAGE IA                             0                             1
  STAGE II                             8                            28
  STAGE IIA                           25                           140
  STAGE IIB                            0                            10
  STAGE IIC                            2                             1
  STAGE III                            6                            20
  STAGE IIIA                           5                            17
  STAGE IIIB                          20                            56
  STAGE IIIC                          20                            32
  STAGE IV                            14                            46
  STAGE IVA                            5                            20
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  AMP PEAK  2(2Q33.1) MUTATED       3  23  91  13
  AMP PEAK  2(2Q33.1) WILD-TYPE    17  82 312  49
D2V5, multiclass
       clus
vv      AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  T0+T1                           3                            17
  T2                             23                            82
  T3                             91                           312
  T4                             13                            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
  AMP PEAK  2(2Q33.1) MUTATED    60  33  36
  AMP PEAK  2(2Q33.1) WILD-TYPE 275 113  72
D2V6, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  N0                          60                           275
  N1                          33                           113
  N2                          36                            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
  AMP PEAK  2(2Q33.1) MUTATED    90  17   3   0  18
  AMP PEAK  2(2Q33.1) WILD-TYPE 353  55   6   1  40
D2V7, multiclass
     clus
vv    AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  M0                           90                           353
  M1                           17                            55
  M1A                           3                             6
  M1B                           0                             1
  MX                           18                            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"
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    62  69
  AMP PEAK  2(2Q33.1) WILD-TYPE 215 246
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     62   69
  AMP PEAK  2(2Q33.1) WILD-TYPE  215  246
        clus
vv       AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  FEMALE                          62                           215
  MALE                            69                           246
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                     76
  AMP PEAK  2(2Q33.1) WILD-TYPE                  297
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                               8
  AMP PEAK  2(2Q33.1) WILD-TYPE                            47
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                      47
  AMP PEAK  2(2Q33.1) WILD-TYPE                    96
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                                0
  AMP PEAK  2(2Q33.1) WILD-TYPE                             13
D2V9, multiclass
                                clus
vv                               AMP PEAK  2(2Q33.1) MUTATED
  COLON ADENOCARCINOMA                                    76
  COLON MUCINOUS ADENOCARCINOMA                            8
  RECTAL ADENOCARCINOMA                                   47
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               AMP PEAK  2(2Q33.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     297
  COLON MUCINOUS ADENOCARCINOMA                             47
  RECTAL ADENOCARCINOMA                                     96
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D2V10, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED     4 127
  AMP PEAK  2(2Q33.1) WILD-TYPE   5 456
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED      4  127
  AMP PEAK  2(2Q33.1) WILD-TYPE    5  456
     clus
vv    AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  NO                            4                             5
  YES                         127                           456
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(2Q33.1) MUTATED    88   2   8   8
  AMP PEAK  2(2Q33.1) WILD-TYPE 338   3  28  19
D2V11, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  R0                          88                           338
  R1                           2                             3
  R2                           8                            28
  RX                           8                            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"
D2V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  2(2Q33.1) MUTATED                                  1     2
  AMP PEAK  2(2Q33.1) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2Q33.1) MUTATED                          12    73
  AMP PEAK  2(2Q33.1) WILD-TYPE                        32   219
D2V13, multiclass
                                  clus
vv                                 AMP PEAK  2(2Q33.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 12
  WHITE                                                     73
                                  clus
vv                                 AMP PEAK  2(2Q33.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   32
  WHITE                                                      219
[1] 4 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(5P12) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  3(5P12) MUTATED    81  25
  AMP PEAK  3(5P12) WILD-TYPE 376  81
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        106                         457 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                         25                          81 
$`AMP PEAK  3(5P12) 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-A6-4107 TCGA-A6-5659 TCGA-A6-6650 TCGA-AA-3488 TCGA-AA-3538 TCGA-AA-3542 
       32.45        30.44        20.61         5.03        26.01        12.99 
TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 
       13.02        24.00         2.01        47.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3856 
       19.00         0.99        37.02        14.93        36.03         0.99 
TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00F 
       17.03        24.03        21.99        50.99        26.01        34.03 
TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W 
       21.99         0.99        51.98         2.96         2.01        41.00 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AY-6196 TCGA-AZ-4614 
       40.96         1.58         0.43         0.92         0.20         5.65 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6603 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CK-5912 
       62.79        49.41        29.56         1.94         2.24        48.20 
TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6167 
        8.02        16.01        15.02        14.04        29.03        14.99 
TCGA-CM-6169 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6538 TCGA-D5-6924 
       13.02        11.01        19.59        17.75        17.13        14.30 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A285 TCGA-DM-A28M 
       13.41        11.38        12.59         7.50         6.12        95.18 
TCGA-F4-6460 TCGA-F4-6855 TCGA-G4-6626 TCGA-G4-6627 TCGA-AF-2687 TCGA-AF-3911 
       13.38        35.41        46.75        47.15        24.13        37.74 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3609 TCGA-AG-3731 
       20.02        10.39         1.02        46.03        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00H 
       17.03        28.04        36.03         1.02        17.03        25.97 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       36.03        12.00        31.00         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6158 
       38.04         0.69         0.72        12.99        15.02         7.10 
TCGA-DC-6683 TCGA-DY-A1DD TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6464 
       10.06        57.24         2.40        16.31        11.51         9.96 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
       14.86         1.02         0.53         0.76 

$`AMP PEAK  3(5P12) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2680 
       37.02        46.65        23.38        17.79        42.28        35.11 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       13.94        15.52        37.05        16.04        34.65        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-A6-6651 
       24.13         8.38        25.08        25.18        24.16        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-3489 
       16.24        24.92        61.84        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-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-3543 TCGA-AA-3544 
       19.07        34.03        29.00        29.00         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        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-3667 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
        6.97        54.02        14.01         0.92        50.04        47.05 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       15.02        11.01        36.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 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-3846 TCGA-AA-3848 
       17.98        15.95        38.99        36.95        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 
       33.07        32.05        31.07        31.07        53.00        27.02 
TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       29.98        18.05        31.00         2.01        12.99        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-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
        2.01        16.08        13.05        34.06        25.02        24.00 
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-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-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-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-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-A02F TCGA-AA-A02J TCGA-AA-A02O 
       26.01        37.02        39.06        39.98         5.03         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       22.03        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-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.20         0.46        14.50        27.09        16.31         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-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-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 
       22.36        65.00        61.41         6.77        12.10       100.01 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74         3.19         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-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        21.01         2.93         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       20.02        37.02        26.04         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 
       29.06        22.03        22.98        30.08        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02        17.03        12.00        16.04        21.99 
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-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        10.06        12.03        14.99        12.26 
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-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 
        7.92        15.12        17.85         4.50        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         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-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-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-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       33.67         1.28         0.53        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-G4-6628 TCGA-NH-A50T 
       13.78        35.80        26.17        91.79        52.80         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        5.06         2.79         5.98         5.59        26.99        17.29 
TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       14.76        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3574 
       12.72        10.39        14.50         8.45        15.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       19.99        14.04         0.99        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W 
       23.01        37.02        15.95         9.07         1.02        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 
       64.01        10.98        51.98        49.97        61.97         0.49 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        1.45         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 
       10.98        11.01        15.02        12.00        13.97        36.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05         5.29       126.44        41.36 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      129.27        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       11.97         8.45        37.51        31.30         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         1.12         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                       0.20                        0.07 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                      95.18                      140.38 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                      16.67                       18.05 
[1] "0.2 - 95.2 (16.7)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.6"
D3V2, continuous
D3V3, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    72  38
  AMP PEAK  3(5P12) WILD-TYPE 357 121
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     72   38
  AMP PEAK  3(5P12) WILD-TYPE  357  121
        clus
vv       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  COLON                         72                         357
  RECTUM                        38                         121
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  3(5P12) MUTATED        18        0        6        26         1
  AMP PEAK  3(5P12) WILD-TYPE      84        1       30       139         9
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(5P12) MUTATED           1         3          5         10
  AMP PEAK  3(5P12) WILD-TYPE         2        23         17         66
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  3(5P12) MUTATED           15       17         5         0
  AMP PEAK  3(5P12) WILD-TYPE         37       43        20         1
D3V4, multiclass
            clus
vv           AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  STAGE I                           18                          84
  STAGE IA                           0                           1
  STAGE II                           6                          30
  STAGE IIA                         26                         139
  STAGE IIB                          1                           9
  STAGE IIC                          1                           2
  STAGE III                          3                          23
  STAGE IIIA                         5                          17
  STAGE IIIB                        10                          66
  STAGE IIIC                        15                          37
  STAGE IV                          17                          43
  STAGE IVA                          5                          20
  STAGE IVB                          0                           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                          T0+T1  T2  T3  T4
  AMP PEAK  3(5P12) MUTATED       2  25  71  12
  AMP PEAK  3(5P12) WILD-TYPE    18  80 332  50
D3V5, multiclass
       clus
vv      AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  T0+T1                         2                          18
  T2                           25                          80
  T3                           71                         332
  T4                           12                          50
[1] 4 2
[1] TRUE
[1] "dimension 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(5P12) MUTATED    53  30  26
  AMP PEAK  3(5P12) WILD-TYPE 282 116  82
D3V6, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  N0                        53                         282
  N1                        30                         116
  N2                        26                          82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  AMP PEAK  3(5P12) MUTATED    76  18   3   0  10
  AMP PEAK  3(5P12) WILD-TYPE 367  54   6   1  48
D3V7, multiclass
     clus
vv    AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  M0                         76                         367
  M1                         18                          54
  M1A                         3                           6
  M1B                         0                           1
  MX                         10                          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"
D3V8, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    50  60
  AMP PEAK  3(5P12) WILD-TYPE 227 255
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     50   60
  AMP PEAK  3(5P12) WILD-TYPE  227  255
        clus
vv       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  FEMALE                        50                         227
  MALE                          60                         255
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                     64
  AMP PEAK  3(5P12) WILD-TYPE                  309
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                               8
  AMP PEAK  3(5P12) WILD-TYPE                            47
                             vv
clus                          RECTAL ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                      38
  AMP PEAK  3(5P12) WILD-TYPE                   105
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                                0
  AMP PEAK  3(5P12) WILD-TYPE                             13
D3V9, multiclass
                                clus
vv                               AMP PEAK  3(5P12) MUTATED
  COLON ADENOCARCINOMA                                  64
  COLON MUCINOUS ADENOCARCINOMA                          8
  RECTAL ADENOCARCINOMA                                 38
  RECTAL MUCINOUS ADENOCARCINOMA                         0
                                clus
vv                               AMP PEAK  3(5P12) WILD-TYPE
  COLON ADENOCARCINOMA                                   309
  COLON MUCINOUS ADENOCARCINOMA                           47
  RECTAL ADENOCARCINOMA                                  105
  RECTAL MUCINOUS ADENOCARCINOMA                          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"
D3V10, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED     3 107
  AMP PEAK  3(5P12) WILD-TYPE   6 476
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED      3  107
  AMP PEAK  3(5P12) WILD-TYPE    6  476
     clus
vv    AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  NO                          3                           6
  YES                       107                         476
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  3(5P12) MUTATED    79   1  13   2
  AMP PEAK  3(5P12) WILD-TYPE 347   4  23  25
D3V11, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  R0                        79                         347
  R1                         1                           4
  R2                        13                          23
  RX                         2                          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"
D3V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  3(5P12) MUTATED                                  0     1
  AMP PEAK  3(5P12) WILD-TYPE                                1    11
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(5P12) MUTATED                           7    53
  AMP PEAK  3(5P12) WILD-TYPE                        37   239
D3V13, multiclass
                                  clus
vv                                 AMP PEAK  3(5P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                7
  WHITE                                                   53
                                  clus
vv                                 AMP PEAK  3(5P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     11
  BLACK OR AFRICAN AMERICAN                                 37
  WHITE                                                    239
[1] 4 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(5Q22.3) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(5Q22.3) MUTATED    54   7
  AMP PEAK  4(5Q22.3) WILD-TYPE 403  99
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                           61                           502 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                            7                            99 
$`AMP PEAK  4(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 
TCGA-AF-6655 TCGA-AG-3609 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A014 
       20.02        19.99         1.02         1.02        25.97        15.95 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       12.00        31.00        38.04         0.49         0.69         0.72 
TCGA-DC-6683 TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6465 
       10.06        20.55        16.31        11.51        11.97        37.51 
TCGA-F5-6811 
        1.02 

$`AMP PEAK  4(5Q22.3) 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-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 
       42.28        35.11        13.94        15.52        37.05        16.04 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       36.53        14.53        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-A6-6651 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-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-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-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-3680 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       47.01        11.01        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 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-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       37.02        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
        0.99        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-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-3977 TCGA-AA-3979 TCGA-AA-3982 
       21.99        16.08        50.99        25.02        24.00        27.02 
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-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-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-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         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-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
        0.20        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-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        22.36        62.79        61.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
      100.01        29.56         5.23         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        21.01 
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-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        30.08        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6168 
       17.03        12.00        29.03        16.04        21.99        12.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        15.02        14.04        11.01        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-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       19.59        13.51        11.51        20.19        20.42        18.25 
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-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       12.00        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       49.91        13.32       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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        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-G4-6307 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-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        91.79        46.75        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 
        2.79         5.98        26.99        17.29        14.76        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       37.74        10.39        14.50         8.45        15.39        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        23.01        37.02        36.03         9.07         1.02 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       38.96        61.97        41.00         1.45         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.46         8.45         9.96        31.30        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                         0.43                          0.07 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                       130.65                        140.38 
  AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE 
                        15.02                         18.05 
[1] "0.4 - 130.7 (15.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.5"
D4V2, continuous
D4V3, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    43  20
  AMP PEAK  4(5Q22.3) WILD-TYPE 386 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     43   20
  AMP PEAK  4(5Q22.3) WILD-TYPE  386  139
        clus
vv       AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  COLON                           43                           386
  RECTUM                          20                           139
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  4(5Q22.3) MUTATED         8        0        2        16         1
  AMP PEAK  4(5Q22.3) WILD-TYPE      94        1       34       149         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(5Q22.3) MUTATED           1         1          2          8
  AMP PEAK  4(5Q22.3) WILD-TYPE         2        25         20         68
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  4(5Q22.3) MUTATED            7        9         5         0
  AMP PEAK  4(5Q22.3) WILD-TYPE         45       51        20         1
D4V4, multiclass
            clus
vv           AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  STAGE I                              8                            94
  STAGE IA                             0                             1
  STAGE II                             2                            34
  STAGE IIA                           16                           149
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            1                            25
  STAGE IIIA                           2                            20
  STAGE IIIB                           8                            68
  STAGE IIIC                           7                            45
  STAGE IV                             9                            51
  STAGE IVA                            5                            20
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  AMP PEAK  4(5Q22.3) MUTATED       1  11  44   7
  AMP PEAK  4(5Q22.3) WILD-TYPE    19  94 359  55
D4V5, multiclass
       clus
vv      AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  T0+T1                           1                            19
  T2                             11                            94
  T3                             44                           359
  T4                              7                            55
[1] 4 2
[1] TRUE
[1] "dimension 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(5Q22.3) MUTATED    30  17  15
  AMP PEAK  4(5Q22.3) WILD-TYPE 305 129  93
D4V6, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  N0                          30                           305
  N1                          17                           129
  N2                          15                            93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  4(5Q22.3) MUTATED    41  12   3   0   5
  AMP PEAK  4(5Q22.3) WILD-TYPE 402  60   6   1  53
D4V7, multiclass
     clus
vv    AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  M0                           41                           402
  M1                           12                            60
  M1A                           3                             6
  M1B                           0                             1
  MX                            5                            53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED    30  33
  AMP PEAK  4(5Q22.3) WILD-TYPE 247 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED     30   33
  AMP PEAK  4(5Q22.3) WILD-TYPE  247  282
        clus
vv       AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  FEMALE                          30                           247
  MALE                            33                           282
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                     40
  AMP PEAK  4(5Q22.3) WILD-TYPE                  333
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                               3
  AMP PEAK  4(5Q22.3) WILD-TYPE                            52
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                      20
  AMP PEAK  4(5Q22.3) WILD-TYPE                   123
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(5Q22.3) MUTATED                                0
  AMP PEAK  4(5Q22.3) WILD-TYPE                             13
D4V9, multiclass
                                clus
vv                               AMP PEAK  4(5Q22.3) MUTATED
  COLON ADENOCARCINOMA                                    40
  COLON MUCINOUS ADENOCARCINOMA                            3
  RECTAL ADENOCARCINOMA                                   20
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               AMP PEAK  4(5Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     333
  COLON MUCINOUS ADENOCARCINOMA                             52
  RECTAL ADENOCARCINOMA                                    123
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D4V10, binary
                               cls
clus                              0   1
  AMP PEAK  4(5Q22.3) MUTATED     1  62
  AMP PEAK  4(5Q22.3) WILD-TYPE   8 521
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(5Q22.3) MUTATED      1   62
  AMP PEAK  4(5Q22.3) WILD-TYPE    8  521
     clus
vv    AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  NO                            1                             8
  YES                          62                           521
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(5Q22.3) MUTATED    44   0   7   0
  AMP PEAK  4(5Q22.3) WILD-TYPE 382   5  29  27
D4V11, multiclass
    clus
vv   AMP PEAK  4(5Q22.3) MUTATED AMP PEAK  4(5Q22.3) WILD-TYPE
  R0                          44                           382
  R1                           0                             5
  R2                           7                            29
  RX                           0                            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"
D4V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  4(5Q22.3) MUTATED                                  0     0
  AMP PEAK  4(5Q22.3) WILD-TYPE                                1    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(5Q22.3) MUTATED                           7    34
  AMP PEAK  4(5Q22.3) WILD-TYPE                        37   258
D4V13, multiclass
                                  clus
vv                                 AMP PEAK  4(5Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     34
                                  clus
vv                                 AMP PEAK  4(5Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   37
  WHITE                                                      258
[1] 4 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(6P21.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(6P21.1) MUTATED   110  26
  AMP PEAK  5(6P21.1) WILD-TYPE 347  80
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                          136                           427 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                           26                            80 
$`AMP PEAK  5(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-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 
       19.99         2.01        15.02        37.05        85.05         0.99 
TCGA-AA-3812 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3930 
       35.05        17.03         0.99        24.03        27.02         2.01 
TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F 
       20.98        21.99        27.02         7.96        13.94        34.03 
TCGA-AA-A00O TCGA-AA-A01I TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6965 
       27.02        31.00         2.96        40.96         1.02         0.20 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4682 
       14.50         0.95         0.20         5.19         5.65        22.36 
TCGA-AZ-4684 TCGA-CA-6719 TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 
       65.00         1.35        15.62        21.99         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 
       29.06        22.98        30.08        16.01         5.03        15.02 
TCGA-CM-6169 TCGA-CM-6170 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 
       13.02        15.02        19.59        13.51        11.51         1.32 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 
       15.12        17.13        12.49         7.53        10.13         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H 
       13.41        11.38        13.32         7.50        14.04       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 
       98.24        95.18         8.61        13.38        13.45         1.55 
TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6310 TCGA-G4-6311 
        0.53        28.21         8.35        82.39        45.11        39.42 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       91.79        46.75        24.13        43.04        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 
       10.39        14.50        15.39         1.02        24.00        46.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 
        6.05        19.99        19.99        29.98         1.02         1.02 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       14.04         1.02         0.99        36.03         9.07        12.00 
TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-4745 
       31.00         0.72        10.19         6.05         9.37        10.98 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE 
       12.99        12.00        15.02        36.00        13.05       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 
       24.13        51.48        20.55        15.85        17.69        37.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6233 TCGA-G5-6641 
       14.86         0.39        18.28        26.43 

$`AMP PEAK  5(6P21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 
        5.06        37.02        46.65        43.76        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       42.28        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.25        16.04        34.65        14.53        32.91        31.63 
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-A6-6140 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       27.09        24.13         8.38        24.16        21.76        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-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       61.84         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-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       26.01         0.99        14.01        33.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3655 TCGA-AA-3660 
       29.95        23.01        20.98        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 
       47.05        47.01        11.01         5.98        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3818 TCGA-AA-3819 
        5.03        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-3842 
        1.02        17.98        15.95        38.99        36.95        37.02 
TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       14.93        33.07        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        17.03        29.98        18.05        31.00 
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-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        16.08        50.99        13.05        34.06 
TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A 
       26.01        25.02        24.00        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-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-A01K 
       15.02        15.02         0.99        32.02        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-A029 TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06        51.98        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-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-A5EK TCGA-AM-5820 TCGA-AM-5821 
        1.58         0.10         0.76         0.43         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       27.09        16.31        15.75        21.44        17.82         5.52 
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-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       83.80        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-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        2.24         3.06         2.14         3.25         3.29         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-5912 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        48.20        51.32        21.01         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-5344 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       27.02        22.03        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-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 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-D5-6529 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-G4-6298 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-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        51.75        35.93        36.72        36.00        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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       52.80         4.11         5.06         2.79         5.98         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       26.99        17.29        14.76        17.95        17.23        13.55 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       12.72         8.45        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 
       32.02         8.02         7.07         2.01         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 
        2.01        50.04        12.03         0.99        15.95         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 
       32.02        19.99        28.04        36.03        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        1.45         0.69         4.60         1.81         6.05         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03         7.99        11.01        15.02 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       13.97         7.10        30.05        12.95        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      126.44        41.36        57.24        32.61         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45         9.96        31.30         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.12         0.76         0.46        55.76 
TCGA-G5-6572 
       47.08 

  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                         0.20                          0.07 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                       129.27                        140.38 
  AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE 
                       15.735                        18.050 
[1] "0.2 - 129.3 (15.7)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.1"
D5V2, continuous
D5V3, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED    95  50
  AMP PEAK  5(6P21.1) WILD-TYPE 334 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED     95   50
  AMP PEAK  5(6P21.1) WILD-TYPE  334  109
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  COLON                           95                           334
  RECTUM                          50                           109
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  5(6P21.1) MUTATED        20        0        4        33         1
  AMP PEAK  5(6P21.1) WILD-TYPE      82        1       32       132         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(6P21.1) MUTATED           1         7          7         24
  AMP PEAK  5(6P21.1) WILD-TYPE         2        19         15         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  5(6P21.1) MUTATED           18       19        11         0
  AMP PEAK  5(6P21.1) WILD-TYPE         34       41        14         1
D5V4, multiclass
            clus
vv           AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  STAGE I                             20                            82
  STAGE IA                             0                             1
  STAGE II                             4                            32
  STAGE IIA                           33                           132
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            7                            19
  STAGE IIIA                           7                            15
  STAGE IIIB                          24                            52
  STAGE IIIC                          18                            34
  STAGE IV                            19                            41
  STAGE IVA                           11                            14
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  AMP PEAK  5(6P21.1) MUTATED       6  19 110  13
  AMP PEAK  5(6P21.1) WILD-TYPE    14  86 293  49
D5V5, multiclass
       clus
vv      AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  T0+T1                           6                            14
  T2                             19                            86
  T3                            110                           293
  T4                             13                            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
  AMP PEAK  5(6P21.1) MUTATED    65  40  42
  AMP PEAK  5(6P21.1) WILD-TYPE 270 106  66
D5V6, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  N0                          65                           270
  N1                          40                           106
  N2                          42                            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  AMP PEAK  5(6P21.1) MUTATED   101  25   4   0  14
  AMP PEAK  5(6P21.1) WILD-TYPE 342  47   5   1  44
D5V7, multiclass
     clus
vv    AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  M0                          101                           342
  M1                           25                            47
  M1A                           4                             5
  M1B                           0                             1
  MX                           14                            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"
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED    61  87
  AMP PEAK  5(6P21.1) WILD-TYPE 216 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED     61   87
  AMP PEAK  5(6P21.1) WILD-TYPE  216  228
        clus
vv       AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  FEMALE                          61                           216
  MALE                            87                           228
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                     89
  AMP PEAK  5(6P21.1) WILD-TYPE                  284
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                               6
  AMP PEAK  5(6P21.1) WILD-TYPE                            49
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                      49
  AMP PEAK  5(6P21.1) WILD-TYPE                    94
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(6P21.1) MUTATED                                1
  AMP PEAK  5(6P21.1) WILD-TYPE                             12
D5V9, multiclass
                                clus
vv                               AMP PEAK  5(6P21.1) MUTATED
  COLON ADENOCARCINOMA                                    89
  COLON MUCINOUS ADENOCARCINOMA                            6
  RECTAL ADENOCARCINOMA                                   49
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK  5(6P21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     284
  COLON MUCINOUS ADENOCARCINOMA                             49
  RECTAL ADENOCARCINOMA                                     94
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D5V10, binary
                               cls
clus                              0   1
  AMP PEAK  5(6P21.1) MUTATED     7 141
  AMP PEAK  5(6P21.1) WILD-TYPE   2 442
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(6P21.1) MUTATED      7  141
  AMP PEAK  5(6P21.1) WILD-TYPE    2  442
     clus
vv    AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  NO                            7                             2
  YES                         141                           442
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(6P21.1) MUTATED   103   0  14   4
  AMP PEAK  5(6P21.1) WILD-TYPE 323   5  22  23
D5V11, multiclass
    clus
vv   AMP PEAK  5(6P21.1) MUTATED AMP PEAK  5(6P21.1) WILD-TYPE
  R0                         103                           323
  R1                           0                             5
  R2                          14                            22
  RX                           4                            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"
D5V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  5(6P21.1) MUTATED                                  1     1
  AMP PEAK  5(6P21.1) WILD-TYPE                                0    11
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(6P21.1) MUTATED                           9    82
  AMP PEAK  5(6P21.1) WILD-TYPE                        35   210
D5V13, multiclass
                                  clus
vv                                 AMP PEAK  5(6P21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  9
  WHITE                                                     82
                                  clus
vv                                 AMP PEAK  5(6P21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       11
  BLACK OR AFRICAN AMERICAN                                   35
  WHITE                                                      210
[1] 4 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   151  39
  AMP PEAK  6(8P11.23) WILD-TYPE 306  67
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           190                            373 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                            39                             67 
$`AMP PEAK  6(8P11.23) MUTATED`
TCGA-3L-AA1B TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-3807 
        5.06        43.43        17.79        45.60        13.94        34.65 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6648 
       32.45        32.91        32.71        29.16        27.09        25.18 
TCGA-A6-6649 TCGA-A6-6782 TCGA-A6-A5ZU TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       24.16        20.28         9.63        37.05         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3538 
        6.97         1.02        36.03        19.07        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       12.99        33.99        20.98        19.99        78.08         6.05 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3681 
        6.97        54.02        14.01        50.04        47.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       37.05        19.00         5.03        19.04         0.99         0.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3875 
       36.95        17.03        31.07        31.07        24.03        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3975 TCGA-AA-3979 TCGA-AA-A00K TCGA-AA-A00R 
       12.99        24.00        34.06        24.00        18.05         0.99 
TCGA-AA-A00Z TCGA-AA-A01D TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O 
       21.99         0.99         1.02        37.02        51.98         0.92 
TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-6004 TCGA-AY-4070 
        0.07         1.58         0.10         0.43        27.09        16.31 
TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       21.44         5.19         5.65        32.94         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-AZ-6608 
       22.36        62.79        61.41        49.41         3.19         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4948 
        2.24         3.06         2.14         3.29         0.07       102.44 
TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 
       15.62        48.20        51.32         2.01        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
        8.02         8.02        22.98        16.01        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        15.02        29.03        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       12.99        13.02        11.01        11.08        11.08        10.06 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       11.51        20.19         1.32         4.50        17.13        16.14 
TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 TCGA-D5-7000 
        7.53        12.43        14.30         9.04        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28H 
      119.70        38.20         7.50        44.32         6.12       117.07 
TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6807 TCGA-G4-6302 TCGA-G4-6303 
       98.24        13.45         6.18        16.24        43.07        61.87 
TCGA-G4-6304 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 
       53.62        45.11        39.42        26.43        46.75        47.15 
TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YX TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 
        4.11         5.59        17.29        37.74        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3887 
       36.03         1.02        24.00         2.01         0.99        36.95 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 
       35.01         1.02        48.03        32.02        36.03         1.02 
TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6544 
        0.99        15.95        31.00        51.98        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         9.37         4.73        60.03 
TCGA-CL-5918 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A1DC 
        7.99        15.02        36.00         7.10        13.05        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 
       57.24        24.13        51.48         0.49        17.00        15.85 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 
       16.31        11.51        10.78        37.51        14.86         1.02 
TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        0.69         0.46        18.28        47.08 

$`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-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82         5.52        75.25        50.37        58.39         1.41 
TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00         6.77        12.10       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       11.74         3.25         0.26         0.33         0.10         1.35 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       17.56        40.34        70.16        21.99        21.01         2.93 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
      124.27        23.05        26.04        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       22.03        30.08        17.03        12.00        14.04        16.04 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 
       15.02        14.04        12.95        13.05        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6531 
       14.99        12.26        19.59        13.51        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 
       18.25         7.92        15.12        17.85        12.49        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 
       12.39        10.13         9.44        11.64        13.41         1.51 
TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       12.00        24.43       130.65        92.75        49.91        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59       140.38       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-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 
       95.18         8.61        13.38        11.11        13.64        35.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
        1.55        16.31        29.59        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-G4-6298 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 
       23.51        74.56        44.68        55.04        51.75        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.72        36.00        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.17        91.79        52.80         5.06         2.79         5.98 
TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       26.99        14.76        24.13        17.95        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        12.72        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       15.39        12.00        32.02         8.02         7.07         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       17.03        13.02        14.01        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       37.02        36.03         9.07         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
       41.00         1.45         4.60         1.81        10.19         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        6.97        13.97        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       12.00        13.97        30.05        12.95        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      126.44       129.27        32.61         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       20.91        18.28        17.69        16.34        16.41         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       13.64        17.46        11.97         8.45         9.96        31.30 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 
        0.39         0.66         0.53         1.12         0.76        55.76 
TCGA-G5-6641 
       26.43 

  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 
                        16.655                         18.250 
[1] "0.1 - 119.7 (16.7)" "0.1 - 140.4 (18.2)"
[1] "hr=" "1.2"
D6V2, continuous
D6V3, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED   151  52
  AMP PEAK  6(8P11.23) WILD-TYPE 278 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED    151   52
  AMP PEAK  6(8P11.23) WILD-TYPE  278  107
        clus
vv       AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  COLON                           151                            278
  RECTUM                           52                            107
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  6(8P11.23) MUTATED        37        0       17        50         4
  AMP PEAK  6(8P11.23) WILD-TYPE      65        1       19       115         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(8P11.23) MUTATED           3         8          6         21
  AMP PEAK  6(8P11.23) WILD-TYPE         0        18         16         55
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  6(8P11.23) MUTATED           22       22         9         0
  AMP PEAK  6(8P11.23) WILD-TYPE         30       38        16         1
D6V4, multiclass
            clus
vv           AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  STAGE I                              37                             65
  STAGE IA                              0                              1
  STAGE II                             17                             19
  STAGE IIA                            50                            115
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                             8                             18
  STAGE IIIA                            6                             16
  STAGE IIIB                           21                             55
  STAGE IIIC                           22                             30
  STAGE IV                             22                             38
  STAGE IVA                             9                             16
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK  6(8P11.23) MUTATED       4  38 136  24
  AMP PEAK  6(8P11.23) WILD-TYPE    16  67 267  38
D6V5, multiclass
       clus
vv      AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  T0+T1                            4                             16
  T2                              38                             67
  T3                             136                            267
  T4                              24                             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
  AMP PEAK  6(8P11.23) MUTATED   116  45  40
  AMP PEAK  6(8P11.23) WILD-TYPE 219 101  68
D6V6, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  N0                          116                            219
  N1                           45                            101
  N2                           40                             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  6(8P11.23) MUTATED   146  26   5   0  24
  AMP PEAK  6(8P11.23) WILD-TYPE 297  46   4   1  34
D6V7, multiclass
     clus
vv    AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  M0                           146                            297
  M1                            26                             46
  M1A                            5                              4
  M1B                            0                              1
  MX                            24                             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"
D6V8, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED    91 112
  AMP PEAK  6(8P11.23) WILD-TYPE 186 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED     91  112
  AMP PEAK  6(8P11.23) WILD-TYPE  186  203
        clus
vv       AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  FEMALE                           91                            186
  MALE                            112                            203
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  6(8P11.23) MUTATED                    137
  AMP PEAK  6(8P11.23) WILD-TYPE                  236
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(8P11.23) MUTATED                              14
  AMP PEAK  6(8P11.23) WILD-TYPE                            41
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK  6(8P11.23) MUTATED                      50
  AMP PEAK  6(8P11.23) WILD-TYPE                    93
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(8P11.23) MUTATED                                2
  AMP PEAK  6(8P11.23) WILD-TYPE                             11
D6V9, multiclass
                                clus
vv                               AMP PEAK  6(8P11.23) MUTATED
  COLON ADENOCARCINOMA                                    137
  COLON MUCINOUS ADENOCARCINOMA                            14
  RECTAL ADENOCARCINOMA                                    50
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK  6(8P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                      236
  COLON MUCINOUS ADENOCARCINOMA                              41
  RECTAL ADENOCARCINOMA                                      93
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D6V10, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED     4 199
  AMP PEAK  6(8P11.23) WILD-TYPE   5 384
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED      4  199
  AMP PEAK  6(8P11.23) WILD-TYPE    5  384
     clus
vv    AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  NO                             4                              5
  YES                          199                            384
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(8P11.23) MUTATED   139   1  16  13
  AMP PEAK  6(8P11.23) WILD-TYPE 287   4  20  14
D6V11, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  R0                          139                            287
  R1                            1                              4
  R2                           16                             20
  RX                           13                             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"
D6V12, 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     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(8P11.23) MUTATED                          13   112
  AMP PEAK  6(8P11.23) WILD-TYPE                        31   180
D6V13, multiclass
                                  clus
vv                                 AMP PEAK  6(8P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                     112
                                  clus
vv                                 AMP PEAK  6(8P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    31
  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(7) Variable = AMP PEAK  7(8P11.21) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(8P11.21) MUTATED   187  45
  AMP PEAK  7(8P11.21) WILD-TYPE 270  61
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           232                            331 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                            45                             61 
$`AMP PEAK  7(8P11.21) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 
        5.06        37.02        43.76        43.43        17.79        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5662 
       45.60        13.94        34.65        32.45        31.63        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6782 
       32.71        29.16        27.09        25.18        24.16        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       61.84         9.63         1.02        37.05         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 
        6.97         1.02        36.03        19.07        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-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        19.99        19.99        78.08         6.97        54.02 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
       14.01        50.04        47.01        15.02         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       19.00        36.00         5.03        19.04         0.99         0.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3858 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
       36.95        17.03        31.07        24.03        27.02        18.05 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3979 
        2.01        12.99        24.00        16.08        34.06        24.00 
TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A01S 
       19.00        18.05         0.99        17.03        21.99         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6899 
       37.02        51.98         0.92        41.00         0.07         1.58 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A54L 
        0.10         0.43         0.92        27.09        21.44         5.19 
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-6598 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       49.41         5.23        11.74         3.19         1.94         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 
        3.06         2.14         0.07         1.35       102.44        15.62 
TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       48.20        51.32         2.01        20.02        37.02         8.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
        8.02        27.02        22.98        30.08        16.01        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 
        5.03        15.02        15.02        15.02        29.03        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 
       12.99        13.02        11.01        11.08        11.08        10.06 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       11.51        20.19         1.32         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-A28H TCGA-DM-A28K TCGA-F4-6459 
        7.50        44.32         6.12       117.07        98.24         8.61 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 
       13.64        13.45         6.18        16.31        16.24         8.35 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6310 TCGA-G4-6311 
       74.56        43.07        53.62        44.68        45.11        39.42 
TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YX 
       26.43        46.75        47.15         4.11         5.59        17.29 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       20.02        10.39        36.03         1.02        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
        2.01         0.99        32.98         1.02        36.95         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       48.03        32.02        28.04        14.04         1.02         0.99 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y 
       23.01        15.95         9.07         1.02        31.00        64.01 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       51.98         1.94        38.96        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         9.37         4.73        60.03 
TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
        7.99        13.97        15.02        36.00         7.10        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
        0.49        17.00        15.85        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 
       13.64        37.51        14.86         1.02         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

$`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-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 
       29.19        33.53        22.09        22.06        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        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-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-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F 
       33.04        35.01        26.01        39.06         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        2.01         5.03        22.03        39.98        18.05        40.96 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 
       21.37         4.21        56.55         0.79         0.72         1.02 
TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
        0.76         0.20         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 
       15.75         0.20        17.82         5.52        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 
       58.39         1.41         5.65        65.00         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6603 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
      100.01        29.56         3.25         3.29         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 
        0.10        17.56        40.34        70.16        21.99        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5341 
        2.93       124.27        23.05        26.04        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       22.03        17.03        12.00        14.04        16.04        21.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 
       15.02        14.04        12.95        13.05        11.01        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6531 
       14.99        12.26        19.59        13.51        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 
       18.25         7.92        15.12        17.85        12.49        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D4 
        9.44        11.64         1.51        12.00        24.43        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32        12.59       140.38       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-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6703 
       35.97        60.79        95.18        13.38        11.11        35.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        29.59        33.67         1.28         0.53        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 
       19.43       107.67        28.21        82.39        23.51        61.87 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 
       55.04        51.75        35.93        36.72        36.00        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       26.04        13.78        35.80        26.17        91.79        52.80 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-AF-2687 
        5.06         2.79         5.98        26.99        14.76        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3575 
       37.74        10.39        14.50         8.45        15.39        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 
       32.02         8.02         7.07         2.01        46.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         6.05        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98         1.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3909 
       19.99        17.03        13.02        35.01        14.01        19.99 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 
       37.02        36.03        12.00        70.03        10.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
       61.97        41.00         4.60         1.81        10.19         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        6.97        13.97        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DG TCGA-DY-A1H8 
       12.00        30.05        12.95         5.29        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
        2.40        20.55        19.96        20.91        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       16.34        16.41         8.61        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        31.30         0.39         0.66         0.69         0.53 
TCGA-F5-6861 
        1.12 

  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 
                         16.31                          19.07 
[1] "0.1 - 130.7 (16.3)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.1"
D7V2, continuous
D7V3, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED   177  69
  AMP PEAK  7(8P11.21) WILD-TYPE 252  90
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED    177   69
  AMP PEAK  7(8P11.21) WILD-TYPE  252   90
        clus
vv       AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  COLON                           177                            252
  RECTUM                           69                             90
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  7(8P11.21) MUTATED        41        0       21        63         4
  AMP PEAK  7(8P11.21) WILD-TYPE      61        1       15       102         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(8P11.21) MUTATED           3        10          9         27
  AMP PEAK  7(8P11.21) WILD-TYPE         0        16         13         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  7(8P11.21) MUTATED           21       34         8         0
  AMP PEAK  7(8P11.21) WILD-TYPE         31       26        17         1
D7V4, multiclass
            clus
vv           AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  STAGE I                              41                             61
  STAGE IA                              0                              1
  STAGE II                             21                             15
  STAGE IIA                            63                            102
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            10                             16
  STAGE IIIA                            9                             13
  STAGE IIIB                           27                             49
  STAGE IIIC                           21                             31
  STAGE IV                             34                             26
  STAGE IVA                             8                             17
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK  7(8P11.21) MUTATED       5  45 169  26
  AMP PEAK  7(8P11.21) WILD-TYPE    15  60 234  36
D7V5, multiclass
       clus
vv      AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  T0+T1                            5                             15
  T2                              45                             60
  T3                             169                            234
  T4                              26                             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
  AMP PEAK  7(8P11.21) MUTATED   139  55  50
  AMP PEAK  7(8P11.21) WILD-TYPE 196  91  58
D7V6, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  N0                          139                            196
  N1                           55                             91
  N2                           50                             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  7(8P11.21) MUTATED   176  37   5   0  26
  AMP PEAK  7(8P11.21) WILD-TYPE 267  35   4   1  32
D7V7, multiclass
     clus
vv    AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  M0                           176                            267
  M1                            37                             35
  M1A                            5                              4
  M1B                            0                              1
  MX                            26                             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"
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED   107 139
  AMP PEAK  7(8P11.21) WILD-TYPE 170 176
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED    107  139
  AMP PEAK  7(8P11.21) WILD-TYPE  170  176
        clus
vv       AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  FEMALE                          107                            170
  MALE                            139                            176
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  7(8P11.21) MUTATED                    161
  AMP PEAK  7(8P11.21) WILD-TYPE                  212
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(8P11.21) MUTATED                              16
  AMP PEAK  7(8P11.21) WILD-TYPE                            39
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK  7(8P11.21) MUTATED                      64
  AMP PEAK  7(8P11.21) WILD-TYPE                    79
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(8P11.21) MUTATED                                3
  AMP PEAK  7(8P11.21) WILD-TYPE                             10
D7V9, multiclass
                                clus
vv                               AMP PEAK  7(8P11.21) MUTATED
  COLON ADENOCARCINOMA                                    161
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                    64
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK  7(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      212
  COLON MUCINOUS ADENOCARCINOMA                              39
  RECTAL ADENOCARCINOMA                                      79
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED     3 243
  AMP PEAK  7(8P11.21) WILD-TYPE   6 340
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED      3  243
  AMP PEAK  7(8P11.21) WILD-TYPE    6  340
     clus
vv    AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  NO                             3                              6
  YES                          243                            340
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  7(8P11.21) MUTATED   167   2  22  14
  AMP PEAK  7(8P11.21) WILD-TYPE 259   3  14  13
D7V11, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  R0                          167                            259
  R1                            2                              3
  R2                           22                             14
  RX                           14                             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"
D7V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK  7(8P11.21) MUTATED                                  0     5
  AMP PEAK  7(8P11.21) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(8P11.21) MUTATED                          15   132
  AMP PEAK  7(8P11.21) WILD-TYPE                        29   160
D7V13, multiclass
                                  clus
vv                                 AMP PEAK  7(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  15
  WHITE                                                     132
                                  clus
vv                                 AMP PEAK  7(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    29
  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(8) Variable = AMP PEAK  8(8Q12.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(8Q12.1) MUTATED   243  57
  AMP PEAK  8(8Q12.1) WILD-TYPE 214  49
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                          300                           263 
  AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE 
                           57                            49 
$`AMP PEAK  8(8Q12.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 
        5.06        43.76        43.43        17.79        35.11        45.60 
TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 
       13.94        15.52        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-6888 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.07         4.21         1.58         0.10         0.20         0.43 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A54L 
        0.92        27.09        16.31         0.20        21.44         5.19 
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-A6GA TCGA-NH-A6GB TCGA-QG-A5YX TCGA-AF-2687 
       47.15         4.11         5.98         5.59        17.29        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.95        17.23        43.04        12.72        37.74        10.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 
       20.02        10.39        36.03        32.02         1.02        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 
        1.02        46.03         6.05         0.99        19.99         7.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 
        1.02        32.98         1.02        36.95         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       32.02        28.04        14.04         1.02        17.03         0.99 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        37.02        15.95         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02N 
       31.00        70.03        64.01        51.98         1.94        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 
       38.04         0.49         1.45         0.69         0.72        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 
        6.05         9.37         4.73        60.03         7.99        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       12.00        13.97        15.02        36.00         7.10        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 
       10.06       126.44        41.36        57.24        24.13         0.49 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
       17.00        15.85        16.34        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       13.64         9.96        37.51        14.86         0.39         1.02 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

$`AMP PEAK  8(8Q12.1) WILD-TYPE`
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 
       37.02        46.65        23.38        42.28        44.91        37.05 
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       34.65        14.53        30.44        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       22.06        22.52         8.38        20.61        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        16.24        24.92        61.84        52.44 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 
        1.02         3.02        58.03        63.98        13.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
        1.02         9.07        24.03        37.05         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       34.03         0.99        21.01        17.95        29.95        23.01 
TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3672 TCGA-AA-3675 
       19.99        13.94        61.02         2.01         0.92        47.05 
TCGA-AA-3680 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01        19.00        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-3844 
       25.02         1.02        17.98        15.95        38.99        14.93 
TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3877 
        0.99        36.03        32.05        31.07        53.00        31.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3968 
       33.01        26.01        24.00         2.01        20.98        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       50.99        13.05        25.02        19.07         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O 
       38.04        30.02        34.03        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       42.02        14.99        34.98        15.02        15.02         0.99 
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-A01Z TCGA-AA-A024 TCGA-AA-A02F TCGA-AA-A02H 
       35.01        26.01        37.02        39.06        39.98         2.01 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        21.37        56.55 
TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6901 TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-3779 
        0.79         0.72         1.02         0.76         0.46        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4313 TCGA-AZ-4315 
        0.95        15.75        17.82         5.52        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5796 TCGA-CA-5797 
        1.41         5.65         6.77       100.01         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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 
       21.99        21.01         2.93       124.27        23.05        26.04 
TCGA-CM-5344 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       22.03        12.00        16.04        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6530 
       13.05        11.01        12.03        14.99        19.59        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 
       17.75        18.25        17.85        12.49        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.64         1.51        12.00        24.43        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       13.32        12.59       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6461 
       14.04        26.47        81.37       119.93        95.18        11.11 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       35.87         1.55        29.59        33.67         1.28         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6309 
       35.41        19.43       107.67        28.21        82.39        51.75 
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-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-QG-A5YV TCGA-QG-A5Z2 
       91.79        52.80         5.06         2.79        26.99        14.76 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3575 
       13.55        19.10        14.50         8.45        15.39        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        8.02         7.07         2.01        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 
       12.03        15.95        19.99         0.99        29.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99        17.03        13.02        35.01        14.01 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 
       19.99        36.03        20.98        13.94         6.02        36.03 
TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6897 
       12.00        10.98        49.97        38.96        41.00         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 
        1.81         6.05         6.97        13.97        10.98        11.01 
TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG 
       15.02        30.05        12.95         5.29       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       17.69        16.41         8.61        17.46        11.97         8.45 
TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       31.30         0.66         0.69         0.53         1.12 

  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 
                        16.67                         19.59 
[1] "0.1 - 140.4 (16.7)" "0.1 - 139.2 (19.6)"
[1] "hr=" "1.1"
D8V2, continuous
D8V3, binary
                               cls
clus                              0   1
  AMP PEAK  8(8Q12.1) MUTATED   226  92
  AMP PEAK  8(8Q12.1) WILD-TYPE 203  67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q12.1) MUTATED    226   92
  AMP PEAK  8(8Q12.1) WILD-TYPE  203   67
        clus
vv       AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  COLON                          226                           203
  RECTUM                          92                            67
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  8(8Q12.1) MUTATED        48        0       22        84         4
  AMP PEAK  8(8Q12.1) WILD-TYPE      54        1       14        81         6
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(8Q12.1) MUTATED           3        11         12         41
  AMP PEAK  8(8Q12.1) WILD-TYPE         0        15         10         35
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  8(8Q12.1) MUTATED           31       43        12         0
  AMP PEAK  8(8Q12.1) WILD-TYPE         21       17        13         1
D8V4, multiclass
            clus
vv           AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  STAGE I                             48                            54
  STAGE IA                             0                             1
  STAGE II                            22                            14
  STAGE IIA                           84                            81
  STAGE IIB                            4                             6
  STAGE IIC                            3                             0
  STAGE III                           11                            15
  STAGE IIIA                          12                            10
  STAGE IIIB                          41                            35
  STAGE IIIC                          31                            21
  STAGE IV                            43                            17
  STAGE IVA                           12                            13
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  AMP PEAK  8(8Q12.1) MUTATED       7  54 221  35
  AMP PEAK  8(8Q12.1) WILD-TYPE    13  51 182  27
D8V5, multiclass
       clus
vv      AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  T0+T1                           7                            13
  T2                             54                            51
  T3                            221                           182
  T4                             35                            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
  AMP PEAK  8(8Q12.1) MUTATED   171  77  67
  AMP PEAK  8(8Q12.1) WILD-TYPE 164  69  41
D8V6, multiclass
    clus
vv   AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  N0                         171                           164
  N1                          77                            69
  N2                          67                            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  8(8Q12.1) MUTATED   225  48   7   0  34
  AMP PEAK  8(8Q12.1) WILD-TYPE 218  24   2   1  24
D8V7, multiclass
     clus
vv    AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  M0                          225                           218
  M1                           48                            24
  M1A                           7                             2
  M1B                           0                             1
  MX                           34                            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"
D8V8, binary
                               cls
clus                              0   1
  AMP PEAK  8(8Q12.1) MUTATED   144 174
  AMP PEAK  8(8Q12.1) WILD-TYPE 133 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q12.1) MUTATED    144  174
  AMP PEAK  8(8Q12.1) WILD-TYPE  133  141
        clus
vv       AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  FEMALE                         144                           133
  MALE                           174                           141
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  8(8Q12.1) MUTATED                    206
  AMP PEAK  8(8Q12.1) WILD-TYPE                  167
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(8Q12.1) MUTATED                              20
  AMP PEAK  8(8Q12.1) WILD-TYPE                            35
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  8(8Q12.1) MUTATED                      86
  AMP PEAK  8(8Q12.1) WILD-TYPE                    57
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(8Q12.1) MUTATED                                4
  AMP PEAK  8(8Q12.1) WILD-TYPE                              9
D8V9, multiclass
                                clus
vv                               AMP PEAK  8(8Q12.1) MUTATED
  COLON ADENOCARCINOMA                                   206
  COLON MUCINOUS ADENOCARCINOMA                           20
  RECTAL ADENOCARCINOMA                                   86
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               AMP PEAK  8(8Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     167
  COLON MUCINOUS ADENOCARCINOMA                             35
  RECTAL ADENOCARCINOMA                                     57
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D8V10, binary
                               cls
clus                              0   1
  AMP PEAK  8(8Q12.1) MUTATED     8 310
  AMP PEAK  8(8Q12.1) WILD-TYPE   1 273
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(8Q12.1) MUTATED      8  310
  AMP PEAK  8(8Q12.1) WILD-TYPE    1  273
     clus
vv    AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  NO                            8                             1
  YES                         310                           273
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  8(8Q12.1) MUTATED   219   3  26  15
  AMP PEAK  8(8Q12.1) WILD-TYPE 207   2  10  12
D8V11, multiclass
    clus
vv   AMP PEAK  8(8Q12.1) MUTATED AMP PEAK  8(8Q12.1) WILD-TYPE
  R0                         219                           207
  R1                           3                             2
  R2                          26                            10
  RX                          15                            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"
D8V12, 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     7
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(8Q12.1) MUTATED                          24   169
  AMP PEAK  8(8Q12.1) WILD-TYPE                        20   123
D8V13, multiclass
                                  clus
vv                                 AMP PEAK  8(8Q12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 24
  WHITE                                                    169
                                  clus
vv                                 AMP PEAK  8(8Q12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   20
  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(9) Variable = AMP PEAK  9(8Q24.21) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(8Q24.21) MUTATED   269  66
  AMP PEAK  9(8Q24.21) WILD-TYPE 188  40
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                           335                            228 
  AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE 
                            66                             40 
$`AMP PEAK  9(8Q24.21) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2680 
        5.06        37.02        43.76        43.43        17.79        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       45.60        13.94        15.52        37.25        16.04        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5662 
       36.53        32.45        32.91        31.63        29.19        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 
       32.71        29.16        27.09        24.13        25.08        25.18 
TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A56B 
       24.16        20.61        24.69        23.87        20.28        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
        9.63         5.03         1.02        37.05         1.02        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3532 
        6.97         1.02        24.03        36.03        19.07        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-3552 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 
       13.02        24.00        23.01        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-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       15.02         5.98        37.05        36.00         5.03        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       19.04         0.99         0.99        36.95        37.02        17.03 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
       33.07        36.03         0.99        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 
       27.02        29.98        18.05         2.01        12.99        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 
       20.98        34.03         2.01        16.08        34.06        26.01 
TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R 
       24.00        27.02        13.94        19.00        18.05         0.99 
TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01K 
       17.03        21.99        15.02         0.99        12.00        31.00 
TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
        1.02        37.02        51.98         2.96         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6899 
        0.92        41.00         0.07        21.37         4.21         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 
        1.02         0.10         0.20         0.43         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4614 
       16.31         0.20        21.44         5.19        75.25         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-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-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
        3.19         1.94         2.24         3.06         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5912 
        0.07         0.10         1.35       102.44        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 
       51.32        21.99         2.01        20.02        37.02         8.02 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 
        8.02        27.02        13.02        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-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        14.04        29.03        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       13.02        11.08        10.06        12.26        19.59        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       11.51        20.19         1.32         7.92        15.12         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       17.13        12.49        16.14        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       12.43        14.30         9.04        13.41        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D9 
      119.70        24.43        38.20       130.65        49.91       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
        7.50        44.32         6.12        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        13.38        13.64        13.45         6.18 
TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 
       16.31        16.24         8.35        23.51        74.56        43.07 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       61.87        53.62        44.68        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       35.93        36.00        26.43        46.75        47.15         4.11 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
        5.59        17.29        24.13        17.95        17.23        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 
       13.55        12.72        37.74        10.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       36.03        32.02         1.02        24.00         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 
        2.01        50.04         6.05         0.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 
        0.99         1.02        32.98         0.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       17.03         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00H 
       36.03        14.04         1.02        17.03         0.99        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       23.01        37.02        15.95         9.07         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
       70.03        64.01        51.98         1.94        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 
       38.04         0.49         1.45         0.69         0.72        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         9.37         4.73        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        7.10        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 
       24.13        32.61         0.49         2.40        17.00        15.85 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 
       16.34        16.31        11.51        10.78        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
       37.51        14.86         0.39         1.02         0.53         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

$`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        21.01 
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         5.06         2.79 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-5654 
        5.98        26.99        14.76        19.10        14.50         8.45 
TCGA-AF-6136 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 
       15.39        12.00         8.02         7.07         2.01        34.03 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 
       12.03        15.95        19.99        29.98         0.99        19.99 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       13.02        35.01        14.01        20.98        13.94         6.02 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AH-6897 
       36.03        12.00        10.98        49.97        38.96         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6160 
        1.81         6.05         6.97        13.97        15.02        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 
       12.95         5.29       129.27        51.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 
       20.91        18.28        17.69        16.41         8.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       11.97         8.45        31.30         0.66         0.69         1.12 

  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 
                         17.03                          19.07 
[1] "0.1 - 140.4 (17.0)" "0.3 - 139.2 (19.1)"
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED   247 105
  AMP PEAK  9(8Q24.21) WILD-TYPE 182  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED    247  105
  AMP PEAK  9(8Q24.21) WILD-TYPE  182   54
        clus
vv       AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  COLON                           247                            182
  RECTUM                          105                             54
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  9(8Q24.21) MUTATED        56        0       24        94         4
  AMP PEAK  9(8Q24.21) WILD-TYPE      46        1       12        71         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(8Q24.21) MUTATED           3        13         15         45
  AMP PEAK  9(8Q24.21) WILD-TYPE         0        13          7         31
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  9(8Q24.21) MUTATED           32       45        14         0
  AMP PEAK  9(8Q24.21) WILD-TYPE         20       15        11         1
D9V4, multiclass
            clus
vv           AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  STAGE I                              56                             46
  STAGE IA                              0                              1
  STAGE II                             24                             12
  STAGE IIA                            94                             71
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            13                             13
  STAGE IIIA                           15                              7
  STAGE IIIB                           45                             31
  STAGE IIIC                           32                             20
  STAGE IV                             45                             15
  STAGE IVA                            14                             11
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK  9(8Q24.21) MUTATED       8  64 245  35
  AMP PEAK  9(8Q24.21) WILD-TYPE    12  41 158  27
D9V5, multiclass
       clus
vv      AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  T0+T1                            8                             12
  T2                              64                             41
  T3                             245                            158
  T4                              35                             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
  AMP PEAK  9(8Q24.21) MUTATED   194  84  72
  AMP PEAK  9(8Q24.21) WILD-TYPE 141  62  36
D9V6, multiclass
    clus
vv   AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  N0                          194                            141
  N1                           84                             62
  N2                           72                             36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK  9(8Q24.21) MUTATED   255  52   7   0  35
  AMP PEAK  9(8Q24.21) WILD-TYPE 188  20   2   1  23
D9V7, multiclass
     clus
vv    AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  M0                           255                            188
  M1                            52                             20
  M1A                            7                              2
  M1B                            0                              1
  MX                            35                             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"
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED   159 194
  AMP PEAK  9(8Q24.21) WILD-TYPE 118 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED    159  194
  AMP PEAK  9(8Q24.21) WILD-TYPE  118  121
        clus
vv       AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  FEMALE                          159                            118
  MALE                            194                            121
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                    221
  AMP PEAK  9(8Q24.21) WILD-TYPE                  152
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                              25
  AMP PEAK  9(8Q24.21) WILD-TYPE                            30
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                      98
  AMP PEAK  9(8Q24.21) WILD-TYPE                    45
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(8Q24.21) MUTATED                                5
  AMP PEAK  9(8Q24.21) WILD-TYPE                              8
D9V9, multiclass
                                clus
vv                               AMP PEAK  9(8Q24.21) MUTATED
  COLON ADENOCARCINOMA                                    221
  COLON MUCINOUS ADENOCARCINOMA                            25
  RECTAL ADENOCARCINOMA                                    98
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK  9(8Q24.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      152
  COLON MUCINOUS ADENOCARCINOMA                              30
  RECTAL ADENOCARCINOMA                                      45
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                                cls
clus                               0   1
  AMP PEAK  9(8Q24.21) MUTATED     8 345
  AMP PEAK  9(8Q24.21) WILD-TYPE   1 238
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(8Q24.21) MUTATED      8  345
  AMP PEAK  9(8Q24.21) WILD-TYPE    1  238
     clus
vv    AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  NO                             8                              1
  YES                          345                            238
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  9(8Q24.21) MUTATED   245   3  27  17
  AMP PEAK  9(8Q24.21) WILD-TYPE 181   2   9  10
D9V11, multiclass
    clus
vv   AMP PEAK  9(8Q24.21) MUTATED AMP PEAK  9(8Q24.21) WILD-TYPE
  R0                          245                            181
  R1                            3                              2
  R2                           27                              9
  RX                           17                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V12, 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     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8Q24.21) MUTATED                          25   184
  AMP PEAK  9(8Q24.21) WILD-TYPE                        19   108
D9V13, multiclass
                                  clus
vv                                 AMP PEAK  9(8Q24.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     184
                                  clus
vv                                 AMP PEAK  9(8Q24.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    19
  WHITE                                                       108
[1] 4 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(10Q22.3) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(10Q22.3) MUTATED    25   8
  AMP PEAK 10(10Q22.3) WILD-TYPE 432  98
  AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE 
                            33                            530 
  AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE 
                             8                             98 
$`AMP PEAK 10(10Q22.3) MUTATED`
TCGA-A6-6649 TCGA-AA-3666 TCGA-AA-3851 TCGA-AA-3869 TCGA-AA-3952 TCGA-AA-3982 
       24.16         2.01        33.07        27.02         2.01        27.02 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AY-A54L TCGA-CM-5860 TCGA-CM-6163 TCGA-CM-6678 
        1.02        35.01         5.19        16.01        14.04        11.01 
TCGA-D5-5539 TCGA-D5-6922 TCGA-D5-6924 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       19.59        10.13        14.30        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A285 TCGA-G4-6299 TCGA-G4-6314 TCGA-G4-6317 
        7.50       131.51         6.12        74.56        35.93        36.00 
TCGA-AF-2689 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3999 TCGA-AG-A01W TCGA-AG-A020 
       17.95        46.03        50.04        28.04        70.03        10.98 
TCGA-BM-6198 TCGA-CI-6619 TCGA-DC-4745 
       10.19         6.05        10.98 

$`AMP PEAK 10(10Q22.3) 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-A6-2683 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-A6-6650 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-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-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        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-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-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.99        36.03        32.05         0.99        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3875 
       31.07        53.00        17.03        24.03        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-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-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-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        31.00        38.07         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-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-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.52        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        21.01         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-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
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-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-D5-5540 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-D5-6535 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-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.39        12.43         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-A1DB TCGA-DM-A1HB 
       38.20       130.65        92.75        49.91        44.32       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-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-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        23.51        43.07        61.87        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       55.04        51.75        45.11        39.42        36.72        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        47.15        52.80         4.11         5.06         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 
        5.98         5.59        26.99        17.29        14.76        24.13 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
        2.01        24.00         1.02        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 
       14.01         1.02        48.03        32.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 
        9.07         1.02        12.00        31.00        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.99        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         7.10        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE 
                          1.02                           0.07 
  AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE 
                        140.38                         139.17 
  AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE 
                        16.010                         17.965 
[1] "1.0 - 140.4 (16.0)" "0.1 - 139.2 (18.0)"
[1] "hr=" "1.1"
D10V2, continuous
D10V3, binary
                                cls
clus                               0   1
  AMP PEAK 10(10Q22.3) MUTATED    26  10
  AMP PEAK 10(10Q22.3) WILD-TYPE 403 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(10Q22.3) MUTATED     26   10
  AMP PEAK 10(10Q22.3) WILD-TYPE  403  149
        clus
vv       AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE
  COLON                            26                            403
  RECTUM                           10                            149
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 10(10Q22.3) MUTATED         4        0        2         7         0
  AMP PEAK 10(10Q22.3) WILD-TYPE      98        1       34       158        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(10Q22.3) MUTATED           0         4          2          4
  AMP PEAK 10(10Q22.3) WILD-TYPE         3        22         20         72
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 10(10Q22.3) MUTATED            6        5         1         0
  AMP PEAK 10(10Q22.3) WILD-TYPE         46       55        24         1
D10V4, multiclass
            clus
vv           AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE
  STAGE I                               4                             98
  STAGE IA                              0                              1
  STAGE II                              2                             34
  STAGE IIA                             7                            158
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             4                             22
  STAGE IIIA                            2                             20
  STAGE IIIB                            4                             72
  STAGE IIIC                            6                             46
  STAGE IV                              5                             55
  STAGE IVA                             1                             24
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 10(10Q22.3) MUTATED       1   3  30   2
  AMP PEAK 10(10Q22.3) WILD-TYPE    19 102 373  60
D10V5, multiclass
       clus
vv      AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE
  T0+T1                            1                             19
  T2                               3                            102
  T3                              30                            373
  T4                               2                             60
[1] 4 2
[1] TRUE
[1] "dimension 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(10Q22.3) MUTATED    13  11  12
  AMP PEAK 10(10Q22.3) WILD-TYPE 322 135  96
D10V6, multiclass
    clus
vv   AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE
  N0                           13                            322
  N1                           11                            135
  N2                           12                             96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 10(10Q22.3) MUTATED    26   5   1   0   2
  AMP PEAK 10(10Q22.3) WILD-TYPE 417  67   8   1  56
D10V7, multiclass
     clus
vv    AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE
  M0                            26                            417
  M1                             5                             67
  M1A                            1                              8
  M1B                            0                              1
  MX                             2                             56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(10Q22.3) MUTATED    15  21
  AMP PEAK 10(10Q22.3) WILD-TYPE 262 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(10Q22.3) MUTATED     15   21
  AMP PEAK 10(10Q22.3) WILD-TYPE  262  294
        clus
vv       AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE
  FEMALE                           15                            262
  MALE                             21                            294
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 10(10Q22.3) MUTATED                     23
  AMP PEAK 10(10Q22.3) WILD-TYPE                  350
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(10Q22.3) MUTATED                               3
  AMP PEAK 10(10Q22.3) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 10(10Q22.3) MUTATED                       8
  AMP PEAK 10(10Q22.3) WILD-TYPE                   135
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(10Q22.3) MUTATED                                1
  AMP PEAK 10(10Q22.3) WILD-TYPE                             12
D10V9, multiclass
                                clus
vv                               AMP PEAK 10(10Q22.3) MUTATED
  COLON ADENOCARCINOMA                                     23
  COLON MUCINOUS ADENOCARCINOMA                             3
  RECTAL ADENOCARCINOMA                                     8
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 10(10Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      350
  COLON MUCINOUS ADENOCARCINOMA                              52
  RECTAL ADENOCARCINOMA                                     135
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D10V10, binary
                                cls
clus                               0   1
  AMP PEAK 10(10Q22.3) MUTATED     1  35
  AMP PEAK 10(10Q22.3) WILD-TYPE   8 548
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(10Q22.3) MUTATED      1   35
  AMP PEAK 10(10Q22.3) WILD-TYPE    8  548
     clus
vv    AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE
  NO                             1                              8
  YES                           35                            548
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 10(10Q22.3) MUTATED    24   0   1   1
  AMP PEAK 10(10Q22.3) WILD-TYPE 402   5  35  26
D10V11, multiclass
    clus
vv   AMP PEAK 10(10Q22.3) MUTATED AMP PEAK 10(10Q22.3) WILD-TYPE
  R0                           24                            402
  R1                            0                              5
  R2                            1                             35
  RX                            1                             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"
D10V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 10(10Q22.3) MUTATED                                  0     0
  AMP PEAK 10(10Q22.3) WILD-TYPE                                1    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(10Q22.3) MUTATED                           1    21
  AMP PEAK 10(10Q22.3) WILD-TYPE                        43   271
D10V13, multiclass
                                  clus
vv                                 AMP PEAK 10(10Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      21
                                  clus
vv                                 AMP PEAK 10(10Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    43
  WHITE                                                       271
[1] 4 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(11P15.5) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(11P15.5) MUTATED   101  24
  AMP PEAK 11(11P15.5) WILD-TYPE 356  82
  AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE 
                           125                            438 
  AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE 
                            24                             82 
$`AMP PEAK 11(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-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
        0.46        16.31         0.95        65.00        62.79        29.56 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
        3.19         1.94         2.14         0.07         0.26         1.35 
TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 
      102.44         8.02        30.08        17.03        29.03        21.99 
TCGA-CM-6677 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6898 
       11.08        12.26        13.51         1.32        17.85         7.53 
TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6463 
       13.41        49.91        35.97        60.79        13.38        13.64 
TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6314 
        8.35        74.56        61.87        55.04        45.11        35.93 
TCGA-QG-A5YV TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-5654 
       26.99        17.95        17.23        13.55        10.39         8.45 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 
       20.02        10.39        36.03        12.00         8.02         2.01 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3894 
       46.03        34.03        19.99        19.99         0.99        14.01 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N TCGA-AH-6897 TCGA-BM-6198 
       36.03         1.02        25.97        31.00         4.60        10.19 
TCGA-CI-6623 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        9.37        13.97        11.01        15.02        12.99        12.00 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       36.00        30.05       126.44         0.49         2.40        20.55 
TCGA-EI-6514 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6861 TCGA-G5-6233 
       16.31         0.39         1.02         1.12        18.28 

$`AMP PEAK 11(11P15.5) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 
        5.06        46.65        43.76        23.38        42.28        35.11 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       45.60        13.94        15.52        37.05        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        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-A6-6649 
       29.16        27.09        22.52        24.13         8.38        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-AA-3489 
       20.28        16.24        24.92        61.84        52.44         1.02 
TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02        37.05         1.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3524 
        1.02        13.02        38.99         1.02        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 
        8.05        19.07        29.00        26.01         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 
       33.99        21.01        17.95        29.95        20.98        19.99 
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-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01         0.92        47.05        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00        36.00        85.05        26.99        19.04 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3833 
        0.99         0.99        35.05         0.99         1.02        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 
       38.99        36.95        14.93         0.99        36.03        32.05 
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-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-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       24.00         2.01        34.03         2.01        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-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-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        17.03         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
        0.99        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-A01T TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       33.04        37.02        39.06        51.98         2.96         2.01 
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-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37        56.55         0.79         0.72         1.58 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 
        0.10         0.76         0.20         0.43         0.92        14.50 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        15.75         0.20        21.44        17.82         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.52        75.25        50.37        58.39         1.41         5.65 
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-CA-5254 
        6.77        12.10       100.01         5.23        11.74         2.24 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        3.06         3.25         3.29         0.33         0.10        17.56 
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 
       21.01         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-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        16.01        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 
       15.02        15.02        12.00        14.04        16.04        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-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.01        10.06        12.03        14.99 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        11.51        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        15.12         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-D5-6932 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-A1D7 
      119.70        24.43        38.20       130.65        92.75        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-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 
      119.93       117.07        98.24        95.18         8.61        11.11 
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-G4-6297 TCGA-G4-6298 TCGA-G4-6302 TCGA-G4-6304 
      107.67        28.21        82.39        23.51        43.07        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        51.75        39.42        36.72        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        47.15        52.80         4.11         5.06         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2691 
        5.98         5.59        17.29        14.76        24.13        43.04 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3578 
       19.10        12.72        37.74        14.50        15.39        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
        7.07         1.02        24.00         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3728 
       12.03         6.05         0.99        15.95         7.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        13.02        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 
       32.02        19.99        28.04        14.04        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       36.03         9.07         1.02        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        1.81         6.05         6.05         6.97         4.73        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
        7.99        10.98        13.97        15.02         7.10        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.05        10.06         5.29        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       24.13        51.48        32.61        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
        9.96        37.51        31.30        14.86         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.53         0.76         0.46        55.76        47.08        26.43 

  AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE 
                        126.44                         140.38 
  AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE 
                         17.85                          18.00 
[1] "0.1 - 126.4 (17.9)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.1"
D11V2, continuous
D11V3, binary
                                cls
clus                               0   1
  AMP PEAK 11(11P15.5) MUTATED    87  43
  AMP PEAK 11(11P15.5) WILD-TYPE 342 116
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(11P15.5) MUTATED     87   43
  AMP PEAK 11(11P15.5) WILD-TYPE  342  116
        clus
vv       AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE
  COLON                            87                            342
  RECTUM                           43                            116
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 11(11P15.5) MUTATED        20        0        6        35         2
  AMP PEAK 11(11P15.5) WILD-TYPE      82        1       30       130         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(11P15.5) MUTATED           1         6          7         16
  AMP PEAK 11(11P15.5) WILD-TYPE         2        20         15         60
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 11(11P15.5) MUTATED           13       18         6         0
  AMP PEAK 11(11P15.5) WILD-TYPE         39       42        19         1
D11V4, multiclass
            clus
vv           AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE
  STAGE I                              20                             82
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            35                            130
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             6                             20
  STAGE IIIA                            7                             15
  STAGE IIIB                           16                             60
  STAGE IIIC                           13                             39
  STAGE IV                             18                             42
  STAGE IVA                             6                             19
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 11(11P15.5) MUTATED       6  24  93   9
  AMP PEAK 11(11P15.5) WILD-TYPE    14  81 310  53
D11V5, multiclass
       clus
vv      AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE
  T0+T1                            6                             14
  T2                              24                             81
  T3                              93                            310
  T4                               9                             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"
                                vv
clus                              N0  N1  N2
  AMP PEAK 11(11P15.5) MUTATED    70  34  27
  AMP PEAK 11(11P15.5) WILD-TYPE 265 112  81
D11V6, multiclass
    clus
vv   AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE
  N0                           70                            265
  N1                           34                            112
  N2                           27                             81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 11(11P15.5) MUTATED    98  20   3   0   8
  AMP PEAK 11(11P15.5) WILD-TYPE 345  52   6   1  50
D11V7, multiclass
     clus
vv    AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE
  M0                            98                            345
  M1                            20                             52
  M1A                            3                              6
  M1B                            0                              1
  MX                             8                             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"
D11V8, binary
                                cls
clus                               0   1
  AMP PEAK 11(11P15.5) MUTATED    64  68
  AMP PEAK 11(11P15.5) WILD-TYPE 213 247
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(11P15.5) MUTATED     64   68
  AMP PEAK 11(11P15.5) WILD-TYPE  213  247
        clus
vv       AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE
  FEMALE                           64                            213
  MALE                             68                            247
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 11(11P15.5) MUTATED                     83
  AMP PEAK 11(11P15.5) WILD-TYPE                  290
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(11P15.5) MUTATED                               3
  AMP PEAK 11(11P15.5) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 11(11P15.5) MUTATED                      42
  AMP PEAK 11(11P15.5) WILD-TYPE                   101
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(11P15.5) MUTATED                                1
  AMP PEAK 11(11P15.5) WILD-TYPE                             12
D11V9, multiclass
                                clus
vv                               AMP PEAK 11(11P15.5) MUTATED
  COLON ADENOCARCINOMA                                     83
  COLON MUCINOUS ADENOCARCINOMA                             3
  RECTAL ADENOCARCINOMA                                    42
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 11(11P15.5) WILD-TYPE
  COLON ADENOCARCINOMA                                      290
  COLON MUCINOUS ADENOCARCINOMA                              52
  RECTAL ADENOCARCINOMA                                     101
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D11V10, binary
                                cls
clus                               0   1
  AMP PEAK 11(11P15.5) MUTATED     4 128
  AMP PEAK 11(11P15.5) WILD-TYPE   5 455
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(11P15.5) MUTATED      4  128
  AMP PEAK 11(11P15.5) WILD-TYPE    5  455
     clus
vv    AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE
  NO                             4                              5
  YES                          128                            455
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 11(11P15.5) MUTATED    94   1  10   6
  AMP PEAK 11(11P15.5) WILD-TYPE 332   4  26  21
D11V11, multiclass
    clus
vv   AMP PEAK 11(11P15.5) MUTATED AMP PEAK 11(11P15.5) WILD-TYPE
  R0                           94                            332
  R1                            1                              4
  R2                           10                             26
  RX                            6                             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"
D11V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 11(11P15.5) MUTATED                                  0     4
  AMP PEAK 11(11P15.5) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(11P15.5) MUTATED                           7    64
  AMP PEAK 11(11P15.5) WILD-TYPE                        37   228
D11V13, multiclass
                                  clus
vv                                 AMP PEAK 11(11P15.5) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   7
  WHITE                                                      64
                                  clus
vv                                 AMP PEAK 11(11P15.5) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    37
  WHITE                                                       228
[1] 4 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(12P13.32) MUTATION ANALYSIS
D12V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 12(12P13.32) MUTATED   106  28
  AMP PEAK 12(12P13.32) WILD-TYPE 351  78
  AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE 
                            134                             429 
  AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE 
                             28                              78 
$`AMP PEAK 12(12P13.32) MUTATED`
TCGA-3L-AA1B TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 
        5.06        44.91        13.94        16.04        34.65        14.53 
TCGA-A6-5664 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A566 
       22.09        25.08        20.61        20.12        20.28        24.92 
TCGA-AA-3494 TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 
        1.02        58.03        36.03        29.00        29.00        12.99 
TCGA-AA-3560 TCGA-AA-3660 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       19.99        78.08         0.92        11.01         5.98        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3842 
        5.03        26.99         0.99        35.05         0.99        37.02 
TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3950 
       14.93        33.07        12.99        24.00        26.01        24.00 
TCGA-AA-3952 TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
        2.01        34.03        18.05        12.00        31.00        33.04 
TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 
       51.98         0.92        22.03        39.98        40.96         0.07 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-6598 
        0.10         0.20         0.92         1.41         5.13        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CK-4948 
        6.77        11.74         3.19         1.94         3.06       102.44 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-5349 
       40.34        15.62        51.32        20.02         8.02        30.08 
TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 
       16.01        15.02        15.02        21.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 TCGA-D5-6539 
       11.01        11.01        20.19        17.75         4.50        12.49 
TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-7000 
       15.58        14.30        11.64        13.41        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A28M TCGA-F4-6459 
      119.70        24.43        13.32        44.32        95.18         8.61 
TCGA-F4-6703 TCGA-F4-6805 TCGA-G4-6306 TCGA-G4-6314 TCGA-G4-6323 TCGA-G4-6627 
       35.87        16.31        44.68        35.93        13.78        47.15 
TCGA-NH-A6GB TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
        5.59        19.10        12.72        37.74        14.50         8.45 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 
       10.39        36.03        46.03         2.01         6.05        19.99 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-4001 
        7.99         1.02         1.02        36.95         1.02        36.03 
TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N TCGA-CI-6624 
        0.99        15.95        36.03        38.96        61.97         4.73 
TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 
       60.03        13.05        10.06         5.29       126.44        32.61 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6812 
       19.96        18.28        17.69        13.64        11.97         0.66 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`AMP PEAK 12(12P13.32) 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        21.01         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 
        2.01       124.27        23.05        37.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5861 
       27.02        13.02        29.06        22.03        22.98        15.02 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
        5.03        17.03        15.02        12.00        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 
       16.04        14.99        12.99        15.02        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-D5-6538 TCGA-D5-6540 TCGA-D5-6898 
        7.92        15.12        17.85        17.13        16.14         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6930 
       12.39        10.13        12.43         9.04         9.44         1.51 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
       11.38        38.20       130.65        92.75        49.91        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50       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-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24        13.38        11.11        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-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-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6315 
       53.62        55.04        51.75        45.11        39.42        36.72 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 TCGA-G4-6588 
       36.00        26.43        22.09        26.04        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       91.79        46.75        52.80         4.11         5.06         2.79 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 
        5.98        26.99        17.29        14.76        24.13        17.95 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 
       17.23        43.04        13.55        10.39        15.39        20.02 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       24.00         1.02        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       15.95        19.99         0.99        29.98        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       37.02         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X 
       64.01        10.98        51.98        49.97         1.94        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       13.97         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
       12.95        41.36        57.24       129.27        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 
        0.49         2.40        20.55        20.91        17.00        15.85 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         1.02         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.46        55.76        47.08 

  AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE 
                         126.44                          140.38 
  AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE 
                         16.025                          18.050 
[1] "0.1 - 126.4 (16.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.3"
D12V2, continuous
D12V3, binary
                                 cls
clus                                0   1
  AMP PEAK 12(12P13.32) MUTATED   106  38
  AMP PEAK 12(12P13.32) WILD-TYPE 323 121
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(12P13.32) MUTATED    106   38
  AMP PEAK 12(12P13.32) WILD-TYPE  323  121
        clus
vv       AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE
  COLON                            106                             323
  RECTUM                            38                             121
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 12(12P13.32) MUTATED        22        1       13        49         2
  AMP PEAK 12(12P13.32) WILD-TYPE      80        0       23       116         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(12P13.32) MUTATED           1         5          7          9
  AMP PEAK 12(12P13.32) WILD-TYPE         2        21         15         67
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(12P13.32) MUTATED           14       15         6         0
  AMP PEAK 12(12P13.32) WILD-TYPE         38       45        19         1
D12V4, multiclass
            clus
vv           AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE
  STAGE I                               22                              80
  STAGE IA                               1                               0
  STAGE II                              13                              23
  STAGE IIA                             49                             116
  STAGE IIB                              2                               8
  STAGE IIC                              1                               2
  STAGE III                              5                              21
  STAGE IIIA                             7                              15
  STAGE IIIB                             9                              67
  STAGE IIIC                            14                              38
  STAGE IV                              15                              45
  STAGE IVA                              6                              19
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 12(12P13.32) MUTATED       2  27  98  18
  AMP PEAK 12(12P13.32) WILD-TYPE    18  78 305  44
D12V5, multiclass
       clus
vv      AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE
  T0+T1                             2                              18
  T2                               27                              78
  T3                               98                             305
  T4                               18                              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 12(12P13.32) MUTATED    91  27  28
  AMP PEAK 12(12P13.32) WILD-TYPE 244 119  80
D12V6, multiclass
    clus
vv   AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE
  N0                            91                             244
  N1                            27                             119
  N2                            28                              80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 12(12P13.32) MUTATED   107  14   4   0  20
  AMP PEAK 12(12P13.32) WILD-TYPE 336  58   5   1  38
D12V7, multiclass
     clus
vv    AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE
  M0                            107                             336
  M1                             14                              58
  M1A                             4                               5
  M1B                             0                               1
  MX                             20                              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"
D12V8, binary
                                 cls
clus                                0   1
  AMP PEAK 12(12P13.32) MUTATED    67  79
  AMP PEAK 12(12P13.32) WILD-TYPE 210 236
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(12P13.32) MUTATED     67   79
  AMP PEAK 12(12P13.32) WILD-TYPE  210  236
        clus
vv       AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE
  FEMALE                            67                             210
  MALE                              79                             236
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 12(12P13.32) MUTATED                     95
  AMP PEAK 12(12P13.32) WILD-TYPE                  278
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(12P13.32) MUTATED                              11
  AMP PEAK 12(12P13.32) WILD-TYPE                            44
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 12(12P13.32) MUTATED                      32
  AMP PEAK 12(12P13.32) WILD-TYPE                   111
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(12P13.32) MUTATED                                5
  AMP PEAK 12(12P13.32) WILD-TYPE                              8
D12V9, multiclass
                                clus
vv                               AMP PEAK 12(12P13.32) MUTATED
  COLON ADENOCARCINOMA                                      95
  COLON MUCINOUS ADENOCARCINOMA                             11
  RECTAL ADENOCARCINOMA                                     32
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 12(12P13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                       278
  COLON MUCINOUS ADENOCARCINOMA                               44
  RECTAL ADENOCARCINOMA                                      111
  RECTAL MUCINOUS ADENOCARCINOMA                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                                 cls
clus                                0   1
  AMP PEAK 12(12P13.32) MUTATED     3 143
  AMP PEAK 12(12P13.32) WILD-TYPE   6 440
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(12P13.32) MUTATED      3  143
  AMP PEAK 12(12P13.32) WILD-TYPE    6  440
     clus
vv    AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE
  NO                              3                               6
  YES                           143                             440
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 12(12P13.32) MUTATED   106   1   6   6
  AMP PEAK 12(12P13.32) WILD-TYPE 320   4  30  21
D12V11, multiclass
    clus
vv   AMP PEAK 12(12P13.32) MUTATED AMP PEAK 12(12P13.32) WILD-TYPE
  R0                           106                             320
  R1                             1                               4
  R2                             6                              30
  RX                             6                              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"
D12V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 12(12P13.32) MUTATED                                  0     2
  AMP PEAK 12(12P13.32) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(12P13.32) MUTATED                           8    74
  AMP PEAK 12(12P13.32) WILD-TYPE                        36   218
D12V13, multiclass
                                  clus
vv                                 AMP PEAK 12(12P13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                       74
                                  clus
vv                                 AMP PEAK 12(12P13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     36
  WHITE                                                        218
[1] 4 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(13Q12.13) MUTATION ANALYSIS
D13V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 13(13Q12.13) MUTATED   293  73
  AMP PEAK 13(13Q12.13) WILD-TYPE 164  33
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            366                             197 
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                             73                              33 
$`AMP PEAK 13(13Q12.13) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        5.06        37.02        46.65        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 
       44.91        35.11        45.60        13.94        15.52        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-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       33.53        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-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 
        5.03         1.02        37.05         1.02        58.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3532 
       38.99         9.07        24.03        36.03        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-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-3666 TCGA-AA-3667 TCGA-AA-3673 
       19.99        78.08         6.05         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 
       15.02         5.98        37.05        19.00         5.03        85.05 
TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3841 
        0.99         0.99        35.05         0.99        25.02        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 
       37.02        14.93        17.03         0.99        32.05         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-3939 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        12.99        24.00        26.01        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-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       24.00        27.02        19.07         7.96        27.02        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 
       19.00        34.03        17.03        42.02        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
       15.02         0.99        32.02        12.00        31.00        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.96        39.98         2.01        41.00        39.98        40.96 
TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       21.37         0.79         1.58         1.02         0.10         0.20 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.43        14.50        16.31         0.95        15.75        21.44 
TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 
        5.19        75.25        50.37         1.41         5.13        83.80 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       22.36        65.00        62.79        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 
        5.23        11.74         1.94         2.24         3.06         0.07 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        1.35        17.56       102.44        48.20        21.99         2.01 
TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       20.02         8.02         8.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       22.98        30.08        16.01         5.03        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-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       13.02        15.02        11.01        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 
       10.06        12.26        19.59        13.51        11.51        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32         7.92        15.12        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       17.13        12.49         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04        13.41        12.00        11.38        10.26       119.70 
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-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
        8.61        13.38         6.18        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-G4-6310 
       82.39        23.51        74.56        61.87        44.68        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 
       39.42        35.93        36.00        26.43        35.80        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-QG-A5YV 
       46.75        47.15         4.11         5.06         5.59        26.99 
TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       17.29        24.13        17.95        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       20.02        10.39         7.07         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 
       46.03        34.03         2.01         0.99        19.99        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99        29.98         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07        12.00        51.98        49.97         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 
       38.04         0.49         0.69         0.72         4.60         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       15.02        36.00         7.10        30.05        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

$`AMP PEAK 13(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        21.01         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-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-AF-3400 TCGA-AG-3574 
       52.80         2.79         5.98        14.76        12.72        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3584 TCGA-AG-3598 TCGA-AG-3599 
       12.00        32.02         8.02        24.00        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
        6.05        15.95         7.99         1.02        32.98         0.99 
TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01N 
       13.02        48.03        20.98        13.94         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       70.03        64.01        10.98        61.97        41.00         1.45 
TCGA-AH-6903 TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6681 TCGA-DT-5265 TCGA-EI-6507 
        1.81        10.19        13.97        12.95         5.29        19.96 
TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6814 TCGA-F5-6861 
        8.61        13.64        17.46         0.53         1.12 

  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                         131.51                          140.38 
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                          17.18                           19.04 
[1] "0.1 - 131.5 (17.2)" "0.1 - 140.4 (19.0)"
[1] "hr=" "1.3"
D13V2, continuous
D13V3, binary
                                 cls
clus                                0   1
  AMP PEAK 13(13Q12.13) MUTATED   260 120
  AMP PEAK 13(13Q12.13) WILD-TYPE 169  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(13Q12.13) MUTATED    260  120
  AMP PEAK 13(13Q12.13) WILD-TYPE  169   39
        clus
vv       AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  COLON                            260                             169
  RECTUM                           120                              39
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 13(13Q12.13) MUTATED        63        0       16        94         4
  AMP PEAK 13(13Q12.13) WILD-TYPE      39        1       20        71         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(13Q12.13) MUTATED           3        15         17         56
  AMP PEAK 13(13Q12.13) WILD-TYPE         0        11          5         20
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(13Q12.13) MUTATED           37       49        22         0
  AMP PEAK 13(13Q12.13) WILD-TYPE         15       11         3         1
D13V4, multiclass
            clus
vv           AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  STAGE I                               63                              39
  STAGE IA                               0                               1
  STAGE II                              16                              20
  STAGE IIA                             94                              71
  STAGE IIB                              4                               6
  STAGE IIC                              3                               0
  STAGE III                             15                              11
  STAGE IIIA                            17                               5
  STAGE IIIB                            56                              20
  STAGE IIIC                            37                              15
  STAGE IV                              49                              11
  STAGE IVA                             22                               3
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 13(13Q12.13) MUTATED      14  64 263  42
  AMP PEAK 13(13Q12.13) WILD-TYPE     6  41 140  20
D13V5, multiclass
       clus
vv      AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  T0+T1                            14                               6
  T2                               64                              41
  T3                              263                             140
  T4                               42                              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 13(13Q12.13) MUTATED   190 111  81
  AMP PEAK 13(13Q12.13) WILD-TYPE 145  35  27
D13V6, multiclass
    clus
vv   AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  N0                           190                             145
  N1                           111                              35
  N2                            81                              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 13(13Q12.13) MUTATED   276  59   8   0  37
  AMP PEAK 13(13Q12.13) WILD-TYPE 167  13   1   1  21
D13V7, multiclass
     clus
vv    AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  M0                            276                             167
  M1                             59                              13
  M1A                             8                               1
  M1B                             0                               1
  MX                             37                              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"
D13V8, binary
                                 cls
clus                                0   1
  AMP PEAK 13(13Q12.13) MUTATED   177 207
  AMP PEAK 13(13Q12.13) WILD-TYPE 100 108
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(13Q12.13) MUTATED    177  207
  AMP PEAK 13(13Q12.13) WILD-TYPE  100  108
        clus
vv       AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  FEMALE                           177                             100
  MALE                             207                             108
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 13(13Q12.13) MUTATED                    244
  AMP PEAK 13(13Q12.13) WILD-TYPE                  129
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(13Q12.13) MUTATED                              16
  AMP PEAK 13(13Q12.13) WILD-TYPE                            39
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 13(13Q12.13) MUTATED                     114
  AMP PEAK 13(13Q12.13) WILD-TYPE                    29
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(13Q12.13) MUTATED                                5
  AMP PEAK 13(13Q12.13) WILD-TYPE                              8
D13V9, multiclass
                                clus
vv                               AMP PEAK 13(13Q12.13) MUTATED
  COLON ADENOCARCINOMA                                     244
  COLON MUCINOUS ADENOCARCINOMA                             16
  RECTAL ADENOCARCINOMA                                    114
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 13(13Q12.13) WILD-TYPE
  COLON ADENOCARCINOMA                                       129
  COLON MUCINOUS ADENOCARCINOMA                               39
  RECTAL ADENOCARCINOMA                                       29
  RECTAL MUCINOUS ADENOCARCINOMA                               8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                                 cls
clus                                0   1
  AMP PEAK 13(13Q12.13) MUTATED     7 377
  AMP PEAK 13(13Q12.13) WILD-TYPE   2 206
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(13Q12.13) MUTATED      7  377
  AMP PEAK 13(13Q12.13) WILD-TYPE    2  206
     clus
vv    AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  NO                              7                               2
  YES                           377                             206
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 13(13Q12.13) MUTATED   271   3  28  12
  AMP PEAK 13(13Q12.13) WILD-TYPE 155   2   8  15
D13V11, multiclass
    clus
vv   AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  R0                           271                             155
  R1                             3                               2
  R2                            28                               8
  RX                            12                              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"
D13V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 13(13Q12.13) MUTATED                                  0     4
  AMP PEAK 13(13Q12.13) WILD-TYPE                                1     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(13Q12.13) MUTATED                          27   204
  AMP PEAK 13(13Q12.13) WILD-TYPE                        17    88
D13V13, multiclass
                                  clus
vv                                 AMP PEAK 13(13Q12.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      204
                                  clus
vv                                 AMP PEAK 13(13Q12.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     17
  WHITE                                                         88
[1] 4 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(13Q12.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(13Q12.2) MUTATED   290  71
  AMP PEAK 14(13Q12.2) WILD-TYPE 167  35
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           361                            202 
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                            71                             35 
$`AMP PEAK 14(13Q12.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        5.06        37.02        46.65        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 
       44.91        35.11        45.60        13.94        15.52        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-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       33.53        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-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 
        5.03         1.02        37.05         1.02        58.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3532 
       38.99         9.07        24.03        36.03        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-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-3666 TCGA-AA-3667 TCGA-AA-3673 
       19.99        78.08         6.05         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 
       15.02         5.98        37.05        19.00        85.05         0.99 
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-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-3866 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3930 TCGA-AA-3939 
       17.03        24.03        27.02        29.98         2.01        12.99 
TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       24.00        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3982 TCGA-AA-3986 
       50.99        13.05        34.06        26.01        27.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L 
        7.96        27.02        13.94        19.00        34.03        17.03 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       42.02        14.99        15.02        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       12.00        31.00        33.04         2.96        39.98         2.01 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 
       41.00        39.98        40.96        21.37         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
        1.02         0.10         0.20         0.43        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
        0.95        15.75        21.44         5.19        75.25        50.37 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       49.41        12.10        29.56         5.23        11.74         1.94 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
        2.24         3.06         0.07         1.35        17.56       102.44 
TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 
       48.20        21.99         2.01        20.02         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-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        17.03        15.02        14.04        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       16.04        14.99        12.99        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.08        11.01        10.06        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       13.51        11.51        17.75        18.25         1.32         7.92 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.50        17.13        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 
       10.13        12.43        14.30         9.04        13.41        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38        10.26       119.70       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 
       13.32         7.50       131.51         7.76         6.12        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 
       26.47       119.93        35.97         8.61        13.38         6.18 
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-G4-6303 
      107.67        28.21         8.35        82.39        23.51        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         5.06 
TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        5.59        26.99        17.29        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        19.10        37.74        10.39        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       15.39        20.02        10.39         7.07         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 
        1.02        46.03        34.03         2.01         0.99        19.99 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       19.99         0.99        29.98         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       36.95        17.03        35.01        14.01         1.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
        0.99         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       36.03         9.07        12.00        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       38.96        41.00        38.04         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        4.60         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       12.00        15.02        36.00         7.10        30.05        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       51.48        32.61         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       16.41        11.51        10.78        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`AMP PEAK 14(13Q12.2) 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-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-3864 TCGA-AA-3875 
       15.95        38.99        33.07        36.03        53.00        18.05 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3977 
       31.00        33.01        24.00         2.01         2.01        25.02 
TCGA-AA-3979 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       24.00        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01K 
       27.02         0.99        17.03        21.99        34.98        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
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-A03F TCGA-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 
       18.05         0.07         4.21        56.55         0.72         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-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       58.39         5.65        32.94        61.41         6.77       100.01 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
        3.19         2.14         3.25         3.29         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
        0.10        40.34        70.16        15.62        51.32        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
        2.93       124.27        23.05        37.02        26.04        27.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6171 TCGA-CM-6674 
       15.02        15.02        12.00        21.99        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6540 
       13.05        12.03        14.99        20.19        20.42        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-DM-A0XD 
       15.58        12.39         9.44        11.64         1.51        24.43 
TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       38.20        12.59       140.38        44.32       135.65       139.17 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 
       81.37        60.79       117.07        98.24        95.18        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-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       74.56        43.07        53.62        55.04        51.75        36.72 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV 
       22.09        26.04        13.78        26.17        52.80         2.79 
TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 
        5.98        14.76        12.72         8.45        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3584 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       32.02         8.02        24.00        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3892 
       15.95         7.99         1.02        32.98         0.99        13.02 
TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       48.03        20.98        13.94         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 
       64.01        10.98        61.97         1.45         1.81        10.19 
TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6681 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 
        6.05        13.97        12.95         5.29        19.96         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6814 TCGA-F5-6861 
       13.64        17.46         0.53         1.12 

  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                        131.51                         140.38 
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                        17.230                         18.545 
[1] "0.1 - 131.5 (17.2)" "0.1 - 140.4 (18.5)"
[1] "hr=" "1.3"
D14V2, continuous
D14V3, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q12.2) MUTATED   256 119
  AMP PEAK 14(13Q12.2) WILD-TYPE 173  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q12.2) MUTATED    256  119
  AMP PEAK 14(13Q12.2) WILD-TYPE  173   40
        clus
vv       AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  COLON                           256                            173
  RECTUM                          119                             40
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 14(13Q12.2) MUTATED        63        0       16        92         4
  AMP PEAK 14(13Q12.2) WILD-TYPE      39        1       20        73         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(13Q12.2) MUTATED           3        15         17         56
  AMP PEAK 14(13Q12.2) WILD-TYPE         0        11          5         20
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 14(13Q12.2) MUTATED           36       48        21         0
  AMP PEAK 14(13Q12.2) WILD-TYPE         16       12         4         1
D14V4, multiclass
            clus
vv           AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  STAGE I                              63                             39
  STAGE IA                              0                              1
  STAGE II                             16                             20
  STAGE IIA                            92                             73
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            15                             11
  STAGE IIIA                           17                              5
  STAGE IIIB                           56                             20
  STAGE IIIC                           36                             16
  STAGE IV                             48                             12
  STAGE IVA                            21                              4
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 14(13Q12.2) MUTATED      14  64 258  42
  AMP PEAK 14(13Q12.2) WILD-TYPE     6  41 145  20
D14V5, multiclass
       clus
vv      AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  T0+T1                           14                              6
  T2                              64                             41
  T3                             258                            145
  T4                              42                             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 14(13Q12.2) MUTATED   188 109  80
  AMP PEAK 14(13Q12.2) WILD-TYPE 147  37  28
D14V6, multiclass
    clus
vv   AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  N0                          188                            147
  N1                          109                             37
  N2                           80                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 14(13Q12.2) MUTATED   273  57   8   0  37
  AMP PEAK 14(13Q12.2) WILD-TYPE 170  15   1   1  21
D14V7, multiclass
     clus
vv    AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  M0                           273                            170
  M1                            57                             15
  M1A                            8                              1
  M1B                            0                              1
  MX                            37                             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"
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q12.2) MUTATED   173 206
  AMP PEAK 14(13Q12.2) WILD-TYPE 104 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q12.2) MUTATED    173  206
  AMP PEAK 14(13Q12.2) WILD-TYPE  104  109
        clus
vv       AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  FEMALE                          173                            104
  MALE                            206                            109
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 14(13Q12.2) MUTATED                    240
  AMP PEAK 14(13Q12.2) WILD-TYPE                  133
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(13Q12.2) MUTATED                              16
  AMP PEAK 14(13Q12.2) WILD-TYPE                            39
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 14(13Q12.2) MUTATED                     113
  AMP PEAK 14(13Q12.2) WILD-TYPE                    30
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(13Q12.2) MUTATED                                5
  AMP PEAK 14(13Q12.2) WILD-TYPE                              8
D14V9, multiclass
                                clus
vv                               AMP PEAK 14(13Q12.2) MUTATED
  COLON ADENOCARCINOMA                                    240
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                   113
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 14(13Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      133
  COLON MUCINOUS ADENOCARCINOMA                              39
  RECTAL ADENOCARCINOMA                                      30
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q12.2) MUTATED     7 372
  AMP PEAK 14(13Q12.2) WILD-TYPE   2 211
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q12.2) MUTATED      7  372
  AMP PEAK 14(13Q12.2) WILD-TYPE    2  211
     clus
vv    AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  NO                             7                              2
  YES                          372                            211
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(13Q12.2) MUTATED   268   3  27  12
  AMP PEAK 14(13Q12.2) WILD-TYPE 158   2   9  15
D14V11, multiclass
    clus
vv   AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  R0                          268                            158
  R1                            3                              2
  R2                           27                              9
  RX                           12                             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"
D14V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 14(13Q12.2) MUTATED                                  0     4
  AMP PEAK 14(13Q12.2) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(13Q12.2) MUTATED                          27   201
  AMP PEAK 14(13Q12.2) WILD-TYPE                        17    91
D14V13, multiclass
                                  clus
vv                                 AMP PEAK 14(13Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  27
  WHITE                                                     201
                                  clus
vv                                 AMP PEAK 14(13Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    17
  WHITE                                                        91
[1] 4 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(13Q22.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(13Q22.1) MUTATED   293  72
  AMP PEAK 15(13Q22.1) WILD-TYPE 164  34
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           365                            198 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                            72                             34 
$`AMP PEAK 15(13Q22.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        5.06        37.02        46.65        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-3807 
       44.91        35.11        45.60        13.94        15.52        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-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       33.53        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-3495 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3511 
        5.03         1.02        37.05         1.02        58.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3532 
       38.99         9.07        24.03        36.03        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-3552 TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       13.02        24.00        20.98        19.99        13.94        19.99 
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-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 
       15.02         5.98        37.05        19.00        85.05         0.99 
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-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03         0.99        32.05         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-3949 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       24.00        26.01         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-3982 
       16.08        50.99        13.05        34.06        26.01        27.02 
TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       19.07         7.96        27.02        13.94        19.00        34.03 
TCGA-AA-A00L TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       17.03        42.02        17.03        14.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01T 
        0.99        32.02        12.00        31.00         1.02        33.04 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.96        39.98         2.01        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
        1.02         0.10         0.20         0.43        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
        0.95        15.75        21.44         5.19        75.25        50.37 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        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-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-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A285 
       49.91        13.32         7.50       131.51         7.76         6.12 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6570 
       14.04        26.47       119.93        35.97        13.38         6.18 
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-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       61.87        44.68        45.11        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        35.80        91.79        46.75        47.15         4.11 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2687 
        5.06         5.98         5.59        26.99        17.29        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        43.04        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3581 
       10.39        14.50        15.39        20.02        10.39         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3605 
        1.02         2.01         1.02        46.03        34.03         0.99 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 
       19.99        19.99         0.99        29.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       17.03         0.99         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
       36.03         9.07        12.00        70.03        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       49.97         1.94        38.96        38.04         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        0.72         4.60         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.99        12.00        15.02        36.00         7.10        30.05 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      129.27        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       16.41        11.51        10.78        11.97         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        18.28        55.76        47.08        26.43 

$`AMP PEAK 15(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 
       21.01         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-A5IV TCGA-QG-A5Z2 
       26.04        13.78        26.17        52.80         2.79        14.76 
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72         8.45        36.03        12.00        32.02         8.02 
TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 
       24.00         2.01        50.04        12.03         6.05        15.95 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3898 
        7.99         1.02        32.98         0.99        13.02        48.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 
       20.98        13.94        37.02         1.02        31.00        10.98 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
       61.97        41.00         1.45         1.81        10.19         6.05 
TCGA-DC-6155 TCGA-DC-6681 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 
       13.97        12.95         2.40        19.96        20.91         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       13.64        17.46         8.45         0.53         1.12         0.46 

  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                          0.07                           0.10 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                        131.51                         140.38 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                         17.13                          19.07 
[1] "0.1 - 131.5 (17.1)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.2"
D15V2, continuous
D15V3, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q22.1) MUTATED   264 114
  AMP PEAK 15(13Q22.1) WILD-TYPE 165  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED    264  114
  AMP PEAK 15(13Q22.1) WILD-TYPE  165   45
        clus
vv       AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  COLON                           264                            165
  RECTUM                          114                             45
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 15(13Q22.1) MUTATED        64        0       20        89         4
  AMP PEAK 15(13Q22.1) WILD-TYPE      38        1       16        76         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(13Q22.1) MUTATED           3        16         17         55
  AMP PEAK 15(13Q22.1) WILD-TYPE         0        10          5         21
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 15(13Q22.1) MUTATED           38       47        20         0
  AMP PEAK 15(13Q22.1) WILD-TYPE         14       13         5         1
D15V4, multiclass
            clus
vv           AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  STAGE I                              64                             38
  STAGE IA                              0                              1
  STAGE II                             20                             16
  STAGE IIA                            89                             76
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            16                             10
  STAGE IIIA                           17                              5
  STAGE IIIB                           55                             21
  STAGE IIIC                           38                             14
  STAGE IV                             47                             13
  STAGE IVA                            20                              5
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 15(13Q22.1) MUTATED      15  65 259  42
  AMP PEAK 15(13Q22.1) WILD-TYPE     5  40 144  20
D15V5, multiclass
       clus
vv      AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  T0+T1                           15                              5
  T2                              65                             40
  T3                             259                            144
  T4                              42                             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 15(13Q22.1) MUTATED   190 110  79
  AMP PEAK 15(13Q22.1) WILD-TYPE 145  36  29
D15V6, multiclass
    clus
vv   AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  N0                          190                            145
  N1                          110                             36
  N2                           79                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 15(13Q22.1) MUTATED   274  56   8   0  40
  AMP PEAK 15(13Q22.1) WILD-TYPE 169  16   1   1  18
D15V7, multiclass
     clus
vv    AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  M0                           274                            169
  M1                            56                             16
  M1A                            8                              1
  M1B                            0                              1
  MX                            40                             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"
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q22.1) MUTATED   171 211
  AMP PEAK 15(13Q22.1) WILD-TYPE 106 104
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED    171  211
  AMP PEAK 15(13Q22.1) WILD-TYPE  106  104
        clus
vv       AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  FEMALE                          171                            106
  MALE                            211                            104
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 15(13Q22.1) MUTATED                    246
  AMP PEAK 15(13Q22.1) WILD-TYPE                  127
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(13Q22.1) MUTATED                              18
  AMP PEAK 15(13Q22.1) WILD-TYPE                            37
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 15(13Q22.1) MUTATED                     109
  AMP PEAK 15(13Q22.1) WILD-TYPE                    34
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(13Q22.1) MUTATED                                4
  AMP PEAK 15(13Q22.1) WILD-TYPE                              9
D15V9, multiclass
                                clus
vv                               AMP PEAK 15(13Q22.1) MUTATED
  COLON ADENOCARCINOMA                                    246
  COLON MUCINOUS ADENOCARCINOMA                            18
  RECTAL ADENOCARCINOMA                                   109
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               AMP PEAK 15(13Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      127
  COLON MUCINOUS ADENOCARCINOMA                              37
  RECTAL ADENOCARCINOMA                                      34
  RECTAL MUCINOUS ADENOCARCINOMA                              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"
D15V10, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q22.1) MUTATED     7 375
  AMP PEAK 15(13Q22.1) WILD-TYPE   2 208
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED      7  375
  AMP PEAK 15(13Q22.1) WILD-TYPE    2  208
     clus
vv    AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  NO                             7                              2
  YES                          375                            208
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(13Q22.1) MUTATED   268   3  26  13
  AMP PEAK 15(13Q22.1) WILD-TYPE 158   2  10  14
D15V11, multiclass
    clus
vv   AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  R0                          268                            158
  R1                            3                              2
  R2                           26                             10
  RX                           13                             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"
D15V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 15(13Q22.1) MUTATED                                  0     5
  AMP PEAK 15(13Q22.1) WILD-TYPE                                1     7
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(13Q22.1) MUTATED                          28   201
  AMP PEAK 15(13Q22.1) WILD-TYPE                        16    91
D15V13, multiclass
                                  clus
vv                                 AMP PEAK 15(13Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  28
  WHITE                                                     201
                                  clus
vv                                 AMP PEAK 15(13Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         7
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                        91
[1] 4 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(15Q26.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(15Q26.1) MUTATED    30  10
  AMP PEAK 16(15Q26.1) WILD-TYPE 427  96
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            40                            523 
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            10                             96 
$`AMP PEAK 16(15Q26.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-6649 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3560 
        5.06        37.02        24.16        29.00        29.00        19.99 
TCGA-AA-3681 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3941 TCGA-AA-A02H TCGA-AY-4070 
        5.98        36.03         0.99        24.00         2.01        16.31 
TCGA-AY-6196 TCGA-AZ-4614 TCGA-CA-5254 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-6161 
        0.20         5.65         2.24        22.98        30.08        15.02 
TCGA-D5-6531 TCGA-D5-6538 TCGA-DM-A1DB TCGA-DM-A288 TCGA-DM-A28A TCGA-G4-6297 
       17.75        17.13        44.32        14.04        26.47        82.39 
TCGA-G4-6299 TCGA-G4-6626 TCGA-QG-A5YV TCGA-AF-3400 TCGA-AG-3587 TCGA-AG-3609 
       74.56        46.75        26.99        12.72        46.03        19.99 
TCGA-AG-3612 TCGA-AG-A01W TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-5918 
       19.99        70.03         0.69        10.19         9.37         7.99 
TCGA-DY-A1DC TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6864 
       41.36         8.45         9.96         0.46 

$`AMP PEAK 16(15Q26.1) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
       46.65        43.76        43.43        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        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-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       24.13         8.38        25.08        25.18        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-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-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        19.07        34.03        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-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-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        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-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-3855 TCGA-AA-3858 
       14.93        17.03         0.99        33.07        32.05        31.07 
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-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        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-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-A004 
       24.00        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-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-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-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        37.02 
TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O 
       39.06        51.98         2.96        39.98         5.03         0.92 
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-6899 
       21.37         4.21        56.55         0.79         0.72         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-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-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-4684 
        1.41        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-5255 
       29.56         5.23        11.74         3.19         1.94         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        21.01         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-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-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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        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-D5-6533 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-D5-6898 TCGA-D5-6920 
        4.50        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-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41         1.51        12.00        11.38        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-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       12.59       140.38         7.50       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17         6.12        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-G4-6302 
       19.43       107.67        28.21         8.35        23.51        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-G4-6627 
       26.04        13.78        35.80        26.17        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       52.80         4.11         5.06         2.79         5.98         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       17.29        14.76        24.13        17.95        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       13.55        19.10        37.74        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       15.95         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81         6.05         6.05         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 
       11.51        10.78        13.64        17.46        11.97        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                          0.20                           0.07 
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                         82.39                         140.38 
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                         18.87                          17.95 
[1] "0.2 - 82.4 (18.9)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "1.4"
D16V2, continuous
D16V3, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.1) MUTATED    29  13
  AMP PEAK 16(15Q26.1) WILD-TYPE 400 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.1) MUTATED     29   13
  AMP PEAK 16(15Q26.1) WILD-TYPE  400  146
        clus
vv       AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  COLON                            29                            400
  RECTUM                           13                            146
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 16(15Q26.1) MUTATED         5        0        1        11         0
  AMP PEAK 16(15Q26.1) WILD-TYPE      97        1       35       154        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(15Q26.1) MUTATED           0         1          0          5
  AMP PEAK 16(15Q26.1) WILD-TYPE         3        25         22         71
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 16(15Q26.1) MUTATED           11        5         3         0
  AMP PEAK 16(15Q26.1) WILD-TYPE         41       55        22         1
D16V4, multiclass
            clus
vv           AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  STAGE I                               5                             97
  STAGE IA                              0                              1
  STAGE II                              1                             35
  STAGE IIA                            11                            154
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             1                             25
  STAGE IIIA                            0                             22
  STAGE IIIB                            5                             71
  STAGE IIIC                           11                             41
  STAGE IV                              5                             55
  STAGE IVA                             3                             22
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 16(15Q26.1) MUTATED       1   4  30   7
  AMP PEAK 16(15Q26.1) WILD-TYPE    19 101 373  55
D16V5, multiclass
       clus
vv      AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  T0+T1                            1                             19
  T2                               4                            101
  T3                              30                            373
  T4                               7                             55
[1] 4 2
[1] TRUE
[1] "dimension 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(15Q26.1) MUTATED    17   8  17
  AMP PEAK 16(15Q26.1) WILD-TYPE 318 138  91
D16V6, multiclass
    clus
vv   AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  N0                           17                            318
  N1                            8                            138
  N2                           17                             91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 16(15Q26.1) MUTATED    31   6   1   0   2
  AMP PEAK 16(15Q26.1) WILD-TYPE 412  66   8   1  56
D16V7, multiclass
     clus
vv    AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  M0                            31                            412
  M1                             6                             66
  M1A                            1                              8
  M1B                            0                              1
  MX                             2                             56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.1) MUTATED    24  18
  AMP PEAK 16(15Q26.1) WILD-TYPE 253 297
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.1) MUTATED     24   18
  AMP PEAK 16(15Q26.1) WILD-TYPE  253  297
        clus
vv       AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  FEMALE                           24                            253
  MALE                             18                            297
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 16(15Q26.1) MUTATED                     25
  AMP PEAK 16(15Q26.1) WILD-TYPE                  348
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(15Q26.1) MUTATED                               4
  AMP PEAK 16(15Q26.1) WILD-TYPE                            51
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 16(15Q26.1) MUTATED                      11
  AMP PEAK 16(15Q26.1) WILD-TYPE                   132
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(15Q26.1) MUTATED                                2
  AMP PEAK 16(15Q26.1) WILD-TYPE                             11
D16V9, multiclass
                                clus
vv                               AMP PEAK 16(15Q26.1) MUTATED
  COLON ADENOCARCINOMA                                     25
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    11
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK 16(15Q26.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      348
  COLON MUCINOUS ADENOCARCINOMA                              51
  RECTAL ADENOCARCINOMA                                     132
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D16V10, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.1) MUTATED     2  40
  AMP PEAK 16(15Q26.1) WILD-TYPE   7 543
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.1) MUTATED      2   40
  AMP PEAK 16(15Q26.1) WILD-TYPE    7  543
     clus
vv    AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  NO                             2                              7
  YES                           40                            543
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(15Q26.1) MUTATED    30   1   3   2
  AMP PEAK 16(15Q26.1) WILD-TYPE 396   4  33  25
D16V11, multiclass
    clus
vv   AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  R0                           30                            396
  R1                            1                              4
  R2                            3                             33
  RX                            2                             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"
D16V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 16(15Q26.1) MUTATED                                  0     1
  AMP PEAK 16(15Q26.1) WILD-TYPE                                1    11
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(15Q26.1) MUTATED                           3    24
  AMP PEAK 16(15Q26.1) WILD-TYPE                        41   268
D16V13, multiclass
                                  clus
vv                                 AMP PEAK 16(15Q26.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      24
                                  clus
vv                                 AMP PEAK 16(15Q26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        11
  BLACK OR AFRICAN AMERICAN                                    41
  WHITE                                                       268
[1] 4 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(16P11.2) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 17(16P11.2) MUTATED   127  27
  AMP PEAK 17(16P11.2) WILD-TYPE 330  79
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                           154                            409 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                            27                             79 
$`AMP PEAK 17(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-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 
        0.20         5.19         5.13        62.79        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 
        1.94         2.24         3.29         1.35       102.44        48.20 
TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       21.99        20.02         8.02        13.02        22.03        22.98 
TCGA-CM-5860 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       16.01        17.03        14.04        29.03        21.99        14.99 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6679 TCGA-D5-5539 TCGA-D5-6532 TCGA-D5-6533 
       15.02        11.01        10.06        19.59        18.25         1.32 
TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6922 TCGA-D5-6929 TCGA-D5-6932 
       15.12        17.13        12.49        10.13        13.41        11.38 
TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 
       38.20        13.32        35.97         8.61        13.38         1.55 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 
       82.39        74.56        61.87        44.68        55.04        45.11 
TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GB 
       39.42        35.93        26.43        13.78        46.75         5.59 
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3582 
       17.95        37.74        10.39        15.39        20.02         1.02 
TCGA-AG-3600 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 
        6.05         7.99         1.02        17.03        19.99        36.03 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
        1.02         0.99        15.95        36.03         9.07        12.00 
TCGA-AG-A01N TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6622 
       31.00        38.96        38.04         0.72        10.19         6.97 
TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 
        9.37        60.03        11.01        12.99        12.00        10.06 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 
       24.13        51.48         0.49        17.69        16.31        37.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
       14.86         0.39         1.02         0.76 

$`AMP PEAK 17(16P11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2682 
        5.06        46.65        43.76        23.38        42.28        13.94 
TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 
       37.05        16.04        34.65        36.53        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-A6-6141 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 
       27.09        22.52         8.38        25.18        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-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-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-3534 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 
       19.07        34.03        29.00         0.99        14.01        21.01 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       17.95        29.95        23.01        20.98        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-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-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-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-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
       38.99         0.99        36.03        32.05        31.07        53.00 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 
       18.05        31.00        33.01        26.01        24.00         2.01 
TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
       21.99        50.99        13.05        34.06        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-A00O 
       30.02        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-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        32.02        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-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-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       22.03        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6964 TCGA-AD-A5EK 
       56.55         0.79         0.72         1.58         0.76         0.43 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 
        0.46         0.92        14.50        27.09        16.31        21.44 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82         5.52        75.25        50.37        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 
        5.65        32.94        83.80        22.36        65.00        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
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-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-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       21.01         2.93         2.01       124.27        23.05        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5861 
        8.02        26.04        27.02        29.06        30.08        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-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.99        13.02        14.04        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        11.01        12.03        14.99        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 
       11.51        20.19        20.42        17.75         7.92        17.85 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 
        4.50        16.14        15.58         7.53        12.39        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-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        24.43       130.65        92.75        49.91 
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-F4-6461 
      119.93        60.79       117.07        98.24        95.18        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-G4-6298 TCGA-G4-6302 TCGA-G4-6304 
      107.67        28.21         8.35        23.51        43.07        53.62 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6586 
       51.75        36.72        36.00        22.09        26.04        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        91.79        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 
        2.79         5.98        26.99        17.29        14.76        24.13 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       17.23        43.04        13.55        19.10        12.72        14.50 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
        8.45        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         0.99        29.98        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
        1.02        48.03        32.02        28.04        14.04        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        61.97        41.00         0.49         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-4957 
        4.60         1.81         6.05         6.05         4.73        13.97 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
        7.99        10.98        15.02        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        30.05        12.95        13.05         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       41.36        57.24       129.27        32.61         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 
       11.97         8.45         9.96        31.30         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                        102.44                         140.38 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                         17.87                          17.95 
[1] "0.1 - 102.4 (17.9)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1"  
D17V2, continuous
D17V3, binary
                                cls
clus                               0   1
  AMP PEAK 17(16P11.2) MUTATED   119  45
  AMP PEAK 17(16P11.2) WILD-TYPE 310 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(16P11.2) MUTATED    119   45
  AMP PEAK 17(16P11.2) WILD-TYPE  310  114
        clus
vv       AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  COLON                           119                            310
  RECTUM                           45                            114
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 17(16P11.2) MUTATED        19        1        4        36         3
  AMP PEAK 17(16P11.2) WILD-TYPE      83        0       32       129         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(16P11.2) MUTATED           0         6         10         31
  AMP PEAK 17(16P11.2) WILD-TYPE         3        20         12         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 17(16P11.2) MUTATED           20       23         7         0
  AMP PEAK 17(16P11.2) WILD-TYPE         32       37        18         1
D17V4, multiclass
            clus
vv           AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  STAGE I                              19                             83
  STAGE IA                              1                              0
  STAGE II                              4                             32
  STAGE IIA                            36                            129
  STAGE IIB                             3                              7
  STAGE IIC                             0                              3
  STAGE III                             6                             20
  STAGE IIIA                           10                             12
  STAGE IIIB                           31                             45
  STAGE IIIC                           20                             32
  STAGE IV                             23                             37
  STAGE IVA                             7                             18
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 17(16P11.2) MUTATED       5  25 118  16
  AMP PEAK 17(16P11.2) WILD-TYPE    15  80 285  46
D17V5, multiclass
       clus
vv      AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  T0+T1                            5                             15
  T2                              25                             80
  T3                             118                            285
  T4                              16                             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 17(16P11.2) MUTATED    69  54  41
  AMP PEAK 17(16P11.2) WILD-TYPE 266  92  67
D17V6, multiclass
    clus
vv   AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  N0                           69                            266
  N1                           54                             92
  N2                           41                             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
  AMP PEAK 17(16P11.2) MUTATED   112  27   3   0  19
  AMP PEAK 17(16P11.2) WILD-TYPE 331  45   6   1  39
D17V7, multiclass
     clus
vv    AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  M0                           112                            331
  M1                            27                             45
  M1A                            3                              6
  M1B                            0                              1
  MX                            19                             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"
D17V8, binary
                                cls
clus                               0   1
  AMP PEAK 17(16P11.2) MUTATED    78  87
  AMP PEAK 17(16P11.2) WILD-TYPE 199 228
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(16P11.2) MUTATED     78   87
  AMP PEAK 17(16P11.2) WILD-TYPE  199  228
        clus
vv       AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  FEMALE                           78                            199
  MALE                             87                            228
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 17(16P11.2) MUTATED                    112
  AMP PEAK 17(16P11.2) WILD-TYPE                  261
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(16P11.2) MUTATED                               7
  AMP PEAK 17(16P11.2) WILD-TYPE                            48
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 17(16P11.2) MUTATED                      45
  AMP PEAK 17(16P11.2) WILD-TYPE                    98
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(16P11.2) MUTATED                                0
  AMP PEAK 17(16P11.2) WILD-TYPE                             13
D17V9, multiclass
                                clus
vv                               AMP PEAK 17(16P11.2) MUTATED
  COLON ADENOCARCINOMA                                    112
  COLON MUCINOUS ADENOCARCINOMA                             7
  RECTAL ADENOCARCINOMA                                    45
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 17(16P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      261
  COLON MUCINOUS ADENOCARCINOMA                              48
  RECTAL ADENOCARCINOMA                                      98
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D17V10, binary
                                cls
clus                               0   1
  AMP PEAK 17(16P11.2) MUTATED     4 161
  AMP PEAK 17(16P11.2) WILD-TYPE   5 422
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(16P11.2) MUTATED      4  161
  AMP PEAK 17(16P11.2) WILD-TYPE    5  422
     clus
vv    AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  NO                             4                              5
  YES                          161                            422
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 17(16P11.2) MUTATED   120   0  14   6
  AMP PEAK 17(16P11.2) WILD-TYPE 306   5  22  21
D17V11, multiclass
    clus
vv   AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  R0                          120                            306
  R1                            0                              5
  R2                           14                             22
  RX                            6                             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"
D17V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 17(16P11.2) MUTATED                                  1     3
  AMP PEAK 17(16P11.2) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(16P11.2) MUTATED                          12    83
  AMP PEAK 17(16P11.2) WILD-TYPE                        32   209
D17V13, multiclass
                                  clus
vv                                 AMP PEAK 17(16P11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  12
  WHITE                                                      83
                                  clus
vv                                 AMP PEAK 17(16P11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    32
  WHITE                                                       209
[1] 4 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(17Q12) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 18(17Q12) MUTATED   122  19
  AMP PEAK 18(17Q12) WILD-TYPE 335  87
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                         141                          422 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                          19                           87 
$`AMP PEAK 18(17Q12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2686 TCGA-A6-3810 
        5.06        43.76        43.43        17.79        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       14.53        30.44        29.19        32.71        29.16        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3494 TCGA-AA-3495 
       25.08        25.18        24.69        20.28         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3517 TCGA-AA-3524 TCGA-AA-3532 TCGA-AA-3542 
        1.02        58.03        38.99        36.03        29.00        12.99 
TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3679 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3812 
       24.00        23.01        15.02        36.00        85.05        35.05 
TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3875 
        1.02        17.03         0.99        24.03        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3982 
       12.99        34.03         2.01        50.99        13.05        27.02 
TCGA-AA-3994 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01S 
       27.02        17.03        21.99        32.02        12.00         1.02 
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-AY-4070 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 
       16.31        61.41        12.10        29.56         3.19         2.24 
TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
        0.07         1.35       102.44         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 
       22.03        17.03        14.04        29.03        21.99        14.99 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 
       13.05        11.08        11.01        19.59        11.51        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 
        1.32        15.12         4.50        17.13        14.30        13.41 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A285 TCGA-DM-A28M TCGA-F4-6704 
       24.43        38.20       130.65         6.12        95.18         1.55 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 
       74.56        61.87        55.04        45.11        39.42        35.93 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A6GB TCGA-QG-A5YX TCGA-AF-2690 
       36.00        26.43        46.75         5.59        17.29        17.23 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3608 
       12.00         7.07         1.02        46.03        34.03        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3898 
       19.99        19.99         0.99        19.99         1.02        48.03 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 
       32.02        36.03         1.02        17.03        15.95         9.07 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 
       31.00        64.01        51.98         0.69         4.60         6.05 
TCGA-CI-6623 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DG 
        9.37        12.00        13.05        10.06         5.29        51.48 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6813 
       17.00        18.28        16.31        11.97         1.02         0.69 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
        0.46        55.76        26.43 

$`AMP PEAK 18(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        21.01         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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5Z2 
        4.11         5.06         2.79         5.98        26.99        14.76 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3584 
       10.39        36.03        32.02         8.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       19.99        28.04        14.04         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J 
        6.02        25.97        23.01        37.02        36.03         1.02 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
       61.97        41.00        38.04         0.49         1.45         0.72 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
        1.81        10.19         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6511 
        0.49         2.40        20.55        19.96        20.91        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       14.86         0.39         0.66         0.53         1.12         0.76 
TCGA-G5-6233 TCGA-G5-6572 
       18.28        47.08 

  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                      130.65                       140.38 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                      17.290                       17.965 
[1] "0.1 - 130.7 (17.3)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.5"
D18V2, continuous
D18V3, binary
                              cls
clus                             0   1
  AMP PEAK 18(17Q12) MUTATED   107  43
  AMP PEAK 18(17Q12) WILD-TYPE 322 116
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED    107   43
  AMP PEAK 18(17Q12) WILD-TYPE  322  116
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  COLON                         107                          322
  RECTUM                         43                          116
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 18(17Q12) MUTATED        22        0        7        37         1
  AMP PEAK 18(17Q12) WILD-TYPE      80        1       29       128         9
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(17Q12) MUTATED           1         5          5         19
  AMP PEAK 18(17Q12) WILD-TYPE         2        21         17         57
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 18(17Q12) MUTATED           17       24         8         1
  AMP PEAK 18(17Q12) WILD-TYPE         35       36        17         0
D18V4, multiclass
            clus
vv           AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  STAGE I                            22                           80
  STAGE IA                            0                            1
  STAGE II                            7                           29
  STAGE IIA                          37                          128
  STAGE IIB                           1                            9
  STAGE IIC                           1                            2
  STAGE III                           5                           21
  STAGE IIIA                          5                           17
  STAGE IIIB                         19                           57
  STAGE IIIC                         17                           35
  STAGE IV                           24                           36
  STAGE IVA                           8                           17
  STAGE IVB                           1                            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                           T0+T1  T2  T3  T4
  AMP PEAK 18(17Q12) MUTATED       8  22 104  16
  AMP PEAK 18(17Q12) WILD-TYPE    12  83 299  46
D18V5, multiclass
       clus
vv      AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  T0+T1                          8                           12
  T2                            22                           83
  T3                           104                          299
  T4                            16                           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 18(17Q12) MUTATED    77  38  34
  AMP PEAK 18(17Q12) WILD-TYPE 258 108  74
D18V6, multiclass
    clus
vv   AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  N0                         77                          258
  N1                         38                          108
  N2                         34                           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
  AMP PEAK 18(17Q12) MUTATED    99  27   4   1  19
  AMP PEAK 18(17Q12) WILD-TYPE 344  45   5   0  39
D18V7, multiclass
     clus
vv    AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  M0                          99                          344
  M1                          27                           45
  M1A                          4                            5
  M1B                          1                            0
  MX                          19                           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"
D18V8, binary
                              cls
clus                             0   1
  AMP PEAK 18(17Q12) MUTATED    61  89
  AMP PEAK 18(17Q12) WILD-TYPE 216 226
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED     61   89
  AMP PEAK 18(17Q12) WILD-TYPE  216  226
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  FEMALE                         61                          216
  MALE                           89                          226
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 18(17Q12) MUTATED                     96
  AMP PEAK 18(17Q12) WILD-TYPE                  277
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(17Q12) MUTATED                              10
  AMP PEAK 18(17Q12) WILD-TYPE                            45
                              vv
clus                           RECTAL ADENOCARCINOMA
  AMP PEAK 18(17Q12) MUTATED                      41
  AMP PEAK 18(17Q12) WILD-TYPE                   102
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(17Q12) MUTATED                                2
  AMP PEAK 18(17Q12) WILD-TYPE                             11
D18V9, multiclass
                                clus
vv                               AMP PEAK 18(17Q12) MUTATED
  COLON ADENOCARCINOMA                                   96
  COLON MUCINOUS ADENOCARCINOMA                          10
  RECTAL ADENOCARCINOMA                                  41
  RECTAL MUCINOUS ADENOCARCINOMA                          2
                                clus
vv                               AMP PEAK 18(17Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    277
  COLON MUCINOUS ADENOCARCINOMA                            45
  RECTAL ADENOCARCINOMA                                   102
  RECTAL MUCINOUS ADENOCARCINOMA                           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"
D18V10, binary
                              cls
clus                             0   1
  AMP PEAK 18(17Q12) MUTATED     1 149
  AMP PEAK 18(17Q12) WILD-TYPE   8 434
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED      1  149
  AMP PEAK 18(17Q12) WILD-TYPE    8  434
     clus
vv    AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  NO                           1                            8
  YES                        149                          434
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 18(17Q12) MUTATED   101   2  16   5
  AMP PEAK 18(17Q12) WILD-TYPE 325   3  20  22
D18V11, multiclass
    clus
vv   AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  R0                        101                          325
  R1                          2                            3
  R2                         16                           20
  RX                          5                           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"
D18V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 18(17Q12) MUTATED                                  1     4
  AMP PEAK 18(17Q12) WILD-TYPE                                0     8
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(17Q12) MUTATED                          11    71
  AMP PEAK 18(17Q12) WILD-TYPE                        33   221
D18V13, multiclass
                                  clus
vv                                 AMP PEAK 18(17Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     4
  BLACK OR AFRICAN AMERICAN                                11
  WHITE                                                    71
                                  clus
vv                                 AMP PEAK 18(17Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       8
  BLACK OR AFRICAN AMERICAN                                  33
  WHITE                                                     221
[1] 4 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(17Q24.1) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(17Q24.1) MUTATED   115  15
  AMP PEAK 19(17Q24.1) WILD-TYPE 342  91
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                           130                            433 
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                            15                             91 
$`AMP PEAK 19(17Q24.1) MUTATED`
TCGA-3L-AA1B TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2686 TCGA-A6-3810 
        5.06        43.43        17.79        42.28        16.04        36.53 
TCGA-A6-4105 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       14.53        30.44        29.19        32.71        29.16        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6782 TCGA-AA-3494 TCGA-AA-3495 
       25.08        25.18        24.69        20.28         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3553 TCGA-AA-3556 TCGA-AA-3679 TCGA-AA-3692 
        1.02        58.03        24.00        23.01        15.02        36.00 
TCGA-AA-3697 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       85.05        35.05         1.02        17.03         0.99        36.03 
TCGA-AA-3856 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3966 
        0.99        24.03        12.99        24.00        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-A02W 
       17.03        21.99        12.00         1.02        37.02        41.00 
TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
        4.21         0.79         0.10         0.43        14.50        16.31 
TCGA-AZ-5407 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4750 
       61.41        29.56         2.24         0.07       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-D5-5538 
       21.99        14.99        13.05        11.08        11.01        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       19.59        11.51         1.32        15.12         4.50        17.13 
TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A1D0 TCGA-DM-A285 TCGA-DM-A28M TCGA-G4-6299 
       14.30        13.41       130.65         6.12        95.18        74.56 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       61.87        55.04        45.11        39.42        35.93        36.00 
TCGA-G4-6320 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A6GB TCGA-QG-A5YX TCGA-AF-2689 
       26.43        91.79        46.75         5.59        17.29        17.95 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3593 
       17.23        13.55        12.00         7.07        46.03        34.03 
TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3882 TCGA-AG-4001 
       50.04        15.95        19.99        19.99        19.99        36.03 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A023 
        1.02        17.03        15.95         9.07        31.00        51.98 
TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 
        0.69         4.60         6.05        12.00        13.05        10.06 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 
      129.27        51.48         0.49         2.40        18.28        16.31 
TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6864 TCGA-G5-6235 
       11.97         1.02         0.46        55.76 

$`AMP PEAK 19(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-3952 TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 
       26.01         2.01        20.98        16.08        26.01        25.02 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       24.00        19.07         7.96        27.02        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-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C 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-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
        1.02        35.01        33.04        35.01        26.01        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-6548 
       22.03        39.98        18.05        40.96         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6964 TCGA-AD-6965 
       56.55         0.72         1.58         1.02         0.76         0.20 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46         0.92        27.09         0.95        15.75         0.20 
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-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        21.01         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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5Z2 
        4.11         5.06         2.79         5.98        26.99        14.76 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       24.13        43.04        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50         8.45        15.39        20.02        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         1.02         2.01        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        2.01        12.03         6.05         0.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
       29.98         1.02        32.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4022 
       48.03        32.02        19.99        28.04        14.04         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         1.02        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
        0.49         1.45         0.72         1.81        10.19         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       10.98        11.01        15.02        12.99        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       36.00         7.10        30.05        12.95         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       41.36        57.24        24.13        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       20.91        17.00        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
        9.96        37.51        31.30        14.86         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 
        0.69         0.53         1.12         0.76        18.28        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                        130.65                         140.38 
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                         17.54                          17.98 
[1] "0.1 - 130.7 (17.5)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.9"
D19V2, continuous
D19V3, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q24.1) MUTATED    98  36
  AMP PEAK 19(17Q24.1) WILD-TYPE 331 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.1) MUTATED     98   36
  AMP PEAK 19(17Q24.1) WILD-TYPE  331  123
        clus
vv       AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  COLON                            98                            331
  RECTUM                           36                            123
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 19(17Q24.1) MUTATED        21        0        4        37         2
  AMP PEAK 19(17Q24.1) WILD-TYPE      81        1       32       128         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(17Q24.1) MUTATED           1         5          4         19
  AMP PEAK 19(17Q24.1) WILD-TYPE         2        21         18         57
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 19(17Q24.1) MUTATED           12       18         8         1
  AMP PEAK 19(17Q24.1) WILD-TYPE         40       42        17         0
D19V4, multiclass
            clus
vv           AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  STAGE I                              21                             81
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            37                            128
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             5                             21
  STAGE IIIA                            4                             18
  STAGE IIIB                           19                             57
  STAGE IIIC                           12                             40
  STAGE IV                             18                             42
  STAGE IVA                             8                             17
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  AMP PEAK 19(17Q24.1) MUTATED       4  24  95  12
  AMP PEAK 19(17Q24.1) WILD-TYPE    16  81 308  50
D19V5, multiclass
       clus
vv      AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  T0+T1                            4                             16
  T2                              24                             81
  T3                              95                            308
  T4                              12                             50
[1] 4 2
[1] TRUE
[1] "dimension 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(17Q24.1) MUTATED    74  35  25
  AMP PEAK 19(17Q24.1) WILD-TYPE 261 111  83
D19V6, multiclass
    clus
vv   AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  N0                           74                            261
  N1                           35                            111
  N2                           25                             83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 19(17Q24.1) MUTATED    92  21   4   1  17
  AMP PEAK 19(17Q24.1) WILD-TYPE 351  51   5   0  41
D19V7, multiclass
     clus
vv    AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  M0                            92                            351
  M1                            21                             51
  M1A                            4                              5
  M1B                            1                              0
  MX                            17                             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"
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q24.1) MUTATED    66  69
  AMP PEAK 19(17Q24.1) WILD-TYPE 211 246
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.1) MUTATED     66   69
  AMP PEAK 19(17Q24.1) WILD-TYPE  211  246
        clus
vv       AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  FEMALE                           66                            211
  MALE                             69                            246
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 19(17Q24.1) MUTATED                     89
  AMP PEAK 19(17Q24.1) WILD-TYPE                  284
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(17Q24.1) MUTATED                               8
  AMP PEAK 19(17Q24.1) WILD-TYPE                            47
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 19(17Q24.1) MUTATED                      36
  AMP PEAK 19(17Q24.1) WILD-TYPE                   107
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(17Q24.1) MUTATED                                0
  AMP PEAK 19(17Q24.1) WILD-TYPE                             13
D19V9, multiclass
                                clus
vv                               AMP PEAK 19(17Q24.1) MUTATED
  COLON ADENOCARCINOMA                                     89
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    36
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 19(17Q24.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      284
  COLON MUCINOUS ADENOCARCINOMA                              47
  RECTAL ADENOCARCINOMA                                     107
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D19V10, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q24.1) MUTATED     1 134
  AMP PEAK 19(17Q24.1) WILD-TYPE   8 449
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.1) MUTATED      1  134
  AMP PEAK 19(17Q24.1) WILD-TYPE    8  449
     clus
vv    AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  NO                             1                              8
  YES                          134                            449
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 19(17Q24.1) MUTATED    96   2  12   3
  AMP PEAK 19(17Q24.1) WILD-TYPE 330   3  24  24
D19V11, multiclass
    clus
vv   AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  R0                           96                            330
  R1                            2                              3
  R2                           12                             24
  RX                            3                             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"
D19V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 19(17Q24.1) MUTATED                                  0     2
  AMP PEAK 19(17Q24.1) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(17Q24.1) MUTATED                          10    71
  AMP PEAK 19(17Q24.1) WILD-TYPE                        34   221
D19V13, multiclass
                                  clus
vv                                 AMP PEAK 19(17Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      71
                                  clus
vv                                 AMP PEAK 19(17Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       221
[1] 4 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(19P13.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(19P13.2) MUTATED    76  19
  AMP PEAK 20(19P13.2) WILD-TYPE 381  87
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            95                            468 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            19                             87 
$`AMP PEAK 20(19P13.2) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2683 
        5.06        37.02        43.43        44.91        45.60        15.52 
TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6651 
       36.53        14.53        31.63        29.16        25.18        21.76 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3519 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3685 
       23.87        52.44         9.07         6.05         2.01        37.05 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3858 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3994 
       35.05         0.99        31.07        50.99        13.05        27.02 
TCGA-AA-A004 TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A029 TCGA-AA-A02O TCGA-AD-6899 
       13.94        42.02        32.02        51.98         0.92         1.58 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 
        1.02         0.43         0.46        16.31        61.41        29.56 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 
       11.74         3.06         1.35        40.34        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
        8.02        13.02        29.06        16.01         5.03        15.02 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6676 
       15.02        14.04        29.03        21.99        13.02        11.08 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6535 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A28F 
       19.59        13.51        15.12        11.38        49.91        35.97 
TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6627 
       74.56        45.11        39.42        36.00        26.43        47.15 
TCGA-AF-2690 TCGA-AF-3913 TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3878 
       17.23        10.39         1.02         6.05        19.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01L 
        1.02        28.04        36.03         1.02         0.99        12.00 
TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 
       31.00         1.94        38.04        10.98        11.01        12.00 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6506 
       36.00        13.05        57.24        24.13         0.49        20.55 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6863 
       17.69        16.31        11.51        11.97         0.76 

$`AMP PEAK 20(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        21.01         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-A50V TCGA-NH-A5IV 
       91.79        46.75        52.80         4.11         5.06         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 
        5.98         5.59        26.99        17.29        14.76        24.13 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50         8.45        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       19.99        14.04        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        13.97        15.02         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE 
       12.95        10.06         5.29       126.44        41.36       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48        32.61         2.40        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       18.28        15.85        16.34        16.41         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.46        18.28        55.76        47.08        26.43 

  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                          0.43                           0.07 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                         74.56                         140.38 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                         16.31                          18.05 
[1] "0.4 - 74.6 (16.3)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.3"
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED    70  34
  AMP PEAK 20(19P13.2) WILD-TYPE 359 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     70   34
  AMP PEAK 20(19P13.2) WILD-TYPE  359  125
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  COLON                            70                            359
  RECTUM                           34                            125
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 20(19P13.2) MUTATED        13        0        6        25         2
  AMP PEAK 20(19P13.2) WILD-TYPE      89        1       30       140         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(19P13.2) MUTATED           1         6          3         20
  AMP PEAK 20(19P13.2) WILD-TYPE         2        20         19         56
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 20(19P13.2) MUTATED            9       12         5         0
  AMP PEAK 20(19P13.2) WILD-TYPE         43       48        20         1
D20V4, multiclass
            clus
vv           AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  STAGE I                              13                             89
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            25                            140
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             6                             20
  STAGE IIIA                            3                             19
  STAGE IIIB                           20                             56
  STAGE IIIC                            9                             43
  STAGE IV                             12                             48
  STAGE IVA                             5                             20
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  AMP PEAK 20(19P13.2) MUTATED       2  14  75  13
  AMP PEAK 20(19P13.2) WILD-TYPE    18  91 328  49
D20V5, multiclass
       clus
vv      AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  T0+T1                            2                             18
  T2                              14                             91
  T3                              75                            328
  T4                              13                             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
  AMP PEAK 20(19P13.2) MUTATED    51  36  17
  AMP PEAK 20(19P13.2) WILD-TYPE 284 110  91
D20V6, multiclass
    clus
vv   AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  N0                           51                            284
  N1                           36                            110
  N2                           17                             91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  AMP PEAK 20(19P13.2) MUTATED    72  14   3   0  14
  AMP PEAK 20(19P13.2) WILD-TYPE 371  58   6   1  44
D20V7, multiclass
     clus
vv    AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  M0                            72                            371
  M1                            14                             58
  M1A                            3                              6
  M1B                            0                              1
  MX                            14                             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"
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED    42  62
  AMP PEAK 20(19P13.2) WILD-TYPE 235 253
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     42   62
  AMP PEAK 20(19P13.2) WILD-TYPE  235  253
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  FEMALE                           42                            235
  MALE                             62                            253
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 20(19P13.2) MUTATED                     64
  AMP PEAK 20(19P13.2) WILD-TYPE                  309
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(19P13.2) MUTATED                               6
  AMP PEAK 20(19P13.2) WILD-TYPE                            49
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 20(19P13.2) MUTATED                      34
  AMP PEAK 20(19P13.2) WILD-TYPE                   109
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(19P13.2) MUTATED                                0
  AMP PEAK 20(19P13.2) WILD-TYPE                             13
D20V9, multiclass
                                clus
vv                               AMP PEAK 20(19P13.2) MUTATED
  COLON ADENOCARCINOMA                                     64
  COLON MUCINOUS ADENOCARCINOMA                             6
  RECTAL ADENOCARCINOMA                                    34
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 20(19P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      309
  COLON MUCINOUS ADENOCARCINOMA                              49
  RECTAL ADENOCARCINOMA                                     109
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D20V10, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED     1 103
  AMP PEAK 20(19P13.2) WILD-TYPE   8 480
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED      1  103
  AMP PEAK 20(19P13.2) WILD-TYPE    8  480
     clus
vv    AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  NO                             1                              8
  YES                          103                            480
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(19P13.2) MUTATED    75   3   6   6
  AMP PEAK 20(19P13.2) WILD-TYPE 351   2  30  21
D20V11, multiclass
    clus
vv   AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  R0                           75                            351
  R1                            3                              2
  R2                            6                             30
  RX                            6                             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"
D20V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 20(19P13.2) MUTATED                                  0     2
  AMP PEAK 20(19P13.2) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(19P13.2) MUTATED                          10    57
  AMP PEAK 20(19P13.2) WILD-TYPE                        34   235
D20V13, multiclass
                                  clus
vv                                 AMP PEAK 20(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      57
                                  clus
vv                                 AMP PEAK 20(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       235
[1] 4 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(19Q12) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(19Q12) MUTATED    99  21
  AMP PEAK 21(19Q12) WILD-TYPE 358  85
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                         120                          443 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                          21                           85 
$`AMP PEAK 21(19Q12) MUTATED`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-2686 
        5.06        37.02        43.43        45.60        15.52        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 
       34.65        36.53        14.53        31.63        29.16        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3502 
       25.18        21.76        23.87        61.84        52.44        35.01 
TCGA-AA-3506 TCGA-AA-3542 TCGA-AA-3552 TCGA-AA-3685 TCGA-AA-3812 TCGA-AA-3818 
       58.03        12.99        13.02        37.05        35.05         0.99 
TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3973 
       37.02        33.07        36.03        12.99        50.99        13.05 
TCGA-AA-A00K TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00Z TCGA-AA-A01G TCGA-AA-A029 
       18.05        27.02        42.02        21.99        12.00        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02O TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 
        2.96        39.98         0.92         4.21         1.58         1.02 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-5407 
        0.20         0.43        14.50         0.20         5.52        61.41 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 
       29.56        11.74         3.06         1.35        40.34        21.99 
TCGA-CK-6748 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-5862 
        2.01        37.02         8.02        13.02        16.01         5.03 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6676 
       15.02        15.02        14.04        29.03        21.99        11.08 
TCGA-D5-5539 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 
       19.59        15.12         4.50        11.64        13.41        12.00 
TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6855 TCGA-G4-6297 
       11.38       119.70        35.97         8.61        35.41        82.39 
TCGA-G4-6299 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6627 TCGA-AF-2689 
       74.56        45.11        39.42        26.43        47.15        17.95 
TCGA-AF-3913 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3878 
       10.39         1.02        46.03         6.05        19.99         0.99 
TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A015 
       19.99         1.02        36.03         1.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-BM-6198 
        9.07        12.00        31.00         1.94        38.04        10.19 
TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 
        6.05         4.73        13.97        10.98        11.01        12.00 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6506 
       36.00        13.05       129.27        24.13         0.49        20.55 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6863 
       17.69        16.31        11.51        13.64        11.97         0.76 

$`AMP PEAK 21(19Q12) 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-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-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01         0.99        14.01        33.99        21.01 
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-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-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-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-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-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-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-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 
       16.08        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-A00L TCGA-AA-A00N TCGA-AA-A00R 
       30.02        34.03        18.05        17.03         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       17.03        14.99        34.98        15.02        15.02         0.99 
TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       32.02        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-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-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.10         0.76         0.46         0.92        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-6598 TCGA-AZ-6599 
       83.80        22.36        65.00        62.79        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10       100.01         5.23         3.19         1.94         2.24 
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-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5912 
        0.10        17.56       102.44        70.16        15.62        48.20 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.01         2.93       124.27        23.05        20.02 
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-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-F4-6463 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-F4-6806 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-F4-6856 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-G4-6303 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-G4-6317 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.72        36.00        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        91.79        46.75        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        1.02        32.98         0.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01W 
        6.02        25.97        23.01        37.02         1.02        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        51.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        1.81         6.05         6.97         9.37        60.03         7.99 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        13.97        15.02         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48        32.61         2.40        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       18.28        15.85        16.34        16.41         8.61        10.78 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                        0.20                         0.07 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                      129.27                       140.38 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                       15.98                        18.05 
[1] "0.2 - 129.3 (16.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1"  
D21V2, continuous
D21V3, binary
                              cls
clus                             0   1
  AMP PEAK 21(19Q12) MUTATED    89  42
  AMP PEAK 21(19Q12) WILD-TYPE 340 117
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(19Q12) MUTATED     89   42
  AMP PEAK 21(19Q12) WILD-TYPE  340  117
        clus
vv       AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  COLON                          89                          340
  RECTUM                         42                          117
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 21(19Q12) MUTATED        21        0        5        32         1
  AMP PEAK 21(19Q12) WILD-TYPE      81        1       31       133         9
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(19Q12) MUTATED           1         5          4         21
  AMP PEAK 21(19Q12) WILD-TYPE         2        21         18         55
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 21(19Q12) MUTATED           11       22         5         0
  AMP PEAK 21(19Q12) WILD-TYPE         41       38        20         1
D21V4, multiclass
            clus
vv           AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  STAGE I                            21                           81
  STAGE IA                            0                            1
  STAGE II                            5                           31
  STAGE IIA                          32                          133
  STAGE IIB                           1                            9
  STAGE IIC                           1                            2
  STAGE III                           5                           21
  STAGE IIIA                          4                           18
  STAGE IIIB                         21                           55
  STAGE IIIC                         11                           41
  STAGE IV                           22                           38
  STAGE IVA                           5                           20
  STAGE IVB                           0                            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                           T0+T1  T2  T3  T4
  AMP PEAK 21(19Q12) MUTATED       3  22  90  16
  AMP PEAK 21(19Q12) WILD-TYPE    17  83 313  46
D21V5, multiclass
       clus
vv      AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  T0+T1                          3                           17
  T2                            22                           83
  T3                            90                          313
  T4                            16                           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 21(19Q12) MUTATED    64  42  24
  AMP PEAK 21(19Q12) WILD-TYPE 271 104  84
D21V6, multiclass
    clus
vv   AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  N0                         64                          271
  N1                         42                          104
  N2                         24                           84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 21(19Q12) MUTATED    87  23   4   0  15
  AMP PEAK 21(19Q12) WILD-TYPE 356  49   5   1  43
D21V7, multiclass
     clus
vv    AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  M0                          87                          356
  M1                          23                           49
  M1A                          4                            5
  M1B                          0                            1
  MX                          15                           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"
D21V8, binary
                              cls
clus                             0   1
  AMP PEAK 21(19Q12) MUTATED    54  77
  AMP PEAK 21(19Q12) WILD-TYPE 223 238
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(19Q12) MUTATED     54   77
  AMP PEAK 21(19Q12) WILD-TYPE  223  238
        clus
vv       AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  FEMALE                         54                          223
  MALE                           77                          238
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 21(19Q12) MUTATED                     81
  AMP PEAK 21(19Q12) WILD-TYPE                  292
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(19Q12) MUTATED                               8
  AMP PEAK 21(19Q12) WILD-TYPE                            47
                              vv
clus                           RECTAL ADENOCARCINOMA
  AMP PEAK 21(19Q12) MUTATED                      42
  AMP PEAK 21(19Q12) WILD-TYPE                   101
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(19Q12) MUTATED                                0
  AMP PEAK 21(19Q12) WILD-TYPE                             13
D21V9, multiclass
                                clus
vv                               AMP PEAK 21(19Q12) MUTATED
  COLON ADENOCARCINOMA                                   81
  COLON MUCINOUS ADENOCARCINOMA                           8
  RECTAL ADENOCARCINOMA                                  42
  RECTAL MUCINOUS ADENOCARCINOMA                          0
                                clus
vv                               AMP PEAK 21(19Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    292
  COLON MUCINOUS ADENOCARCINOMA                            47
  RECTAL ADENOCARCINOMA                                   101
  RECTAL MUCINOUS ADENOCARCINOMA                           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"
D21V10, binary
                              cls
clus                             0   1
  AMP PEAK 21(19Q12) MUTATED     2 129
  AMP PEAK 21(19Q12) WILD-TYPE   7 454
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(19Q12) MUTATED      2  129
  AMP PEAK 21(19Q12) WILD-TYPE    7  454
     clus
vv    AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  NO                           2                            7
  YES                        129                          454
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 21(19Q12) MUTATED    92   2  11   6
  AMP PEAK 21(19Q12) WILD-TYPE 334   3  25  21
D21V11, multiclass
    clus
vv   AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  R0                         92                          334
  R1                          2                            3
  R2                         11                           25
  RX                          6                           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"
D21V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 21(19Q12) MUTATED                                  0     2
  AMP PEAK 21(19Q12) WILD-TYPE                                1    10
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(19Q12) MUTATED                          11    70
  AMP PEAK 21(19Q12) WILD-TYPE                        33   222
D21V13, multiclass
                                  clus
vv                                 AMP PEAK 21(19Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                11
  WHITE                                                    70
                                  clus
vv                                 AMP PEAK 21(19Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                      10
  BLACK OR AFRICAN AMERICAN                                  33
  WHITE                                                     222
[1] 4 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(20P11.23) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 22(20P11.23) MUTATED   242  54
  AMP PEAK 22(20P11.23) WILD-TYPE 215  52
  AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE 
                            296                             267 
  AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE 
                             54                              52 
$`AMP PEAK 22(20P11.23) 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-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       36.53        14.53        32.45        30.44        29.19        29.16 
TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6654 
       27.09        25.08        25.18        24.16        24.69        23.87 
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-3496 TCGA-AA-3506 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3530 TCGA-AA-3532 
        1.02        58.03         6.97         1.02        19.07        29.00 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3558 
       29.00        14.01        21.01        13.02        23.01        20.98 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 
       19.99         6.05         2.01        14.01        50.04        47.05 
TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3811 
       15.02        37.05        19.00        36.00         5.03         0.99 
TCGA-AA-3818 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
        0.99        38.99        37.02        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       33.07         0.99        31.07        17.03        27.02        18.05 
TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       12.99        24.00        34.03         2.01        21.99        16.08 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       50.99        13.05        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-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        33.04        26.01        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 
        2.01         5.03         0.92        41.00        39.98         0.07 
TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       21.37         0.79         0.72         1.58         1.02         0.10 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A69D 
        0.20         0.43        14.50        16.31         5.19         5.52 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        83.80        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         3.19         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        2.14         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       40.34        48.20        20.02         8.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       29.06        22.98         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-6171 
       15.02        14.04        29.03        16.04        21.99        14.04 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       11.01        11.08        11.01        14.99        12.26        19.59 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 
       11.51        20.19        17.75        17.85        12.49         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 
       12.39        10.13         9.04        11.64        13.41        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA 
      119.70        24.43       130.65        12.59         7.50       131.51 
TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17         6.12        14.04       119.93        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
       95.18         8.61        13.38        13.45         6.18         1.55 
TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6307 
       33.67        35.41       107.67        28.21        82.39        55.04 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 
       45.11        39.42        35.93        36.72        26.04        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YV 
       91.79        46.75        47.15         4.11         5.59        26.99 
TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.29        24.13        17.23        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3580 TCGA-AG-3582 
       14.50         8.45        20.02        10.39         8.02         1.02 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 
        1.02        46.03        34.03        50.04        12.03        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       19.99        19.99         7.99        29.98         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
        0.99        36.95        17.03        14.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C 
       19.99        36.03        14.04         1.02        17.03         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       25.97        23.01        37.02        36.03         9.07        12.00 
TCGA-AG-A023 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       51.98        41.00        38.04         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81        10.19         6.05         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       13.97        60.03        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 
       12.00        13.97        15.02        36.00        12.95        13.05 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
      126.44       129.27        51.48         0.49        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.00        18.28        16.31        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       11.97         9.96        37.51         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`AMP PEAK 22(20P11.23) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5656 
       46.65        23.38        42.28        37.05        37.25        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-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 
       22.52        24.13         8.38        20.61        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 
       20.12        19.66        16.24        24.92        52.44         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 
       37.05        35.01        63.98        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-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3553 
       34.03        26.01        12.99         0.99        33.99        24.00 
TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       17.95        29.95        19.99        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        6.97        54.02         0.92        47.01        11.01         5.98 
TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3819 
       85.05        26.99        19.04         0.99        35.05        25.02 
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-3955 TCGA-AA-3975 
       33.01        26.01        24.00         2.01        20.98        34.06 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       25.02        27.02        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 
       18.05        27.02        42.02         0.99        34.98        15.02 
TCGA-AA-A01F TCGA-AA-A01K 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-A01Z TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6888 
       37.02        39.06        22.03        18.05        40.96         4.21 
TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       56.55         0.76         0.46         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 
       15.75         0.20        21.44        17.82        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 
       58.39         5.65        32.94        22.36        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
      100.01         5.23        11.74         3.25         0.33         0.10 
TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      102.44        70.16        15.62        51.32        21.99        21.01 
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-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 
       27.02        22.03        30.08        16.01        15.02        12.00 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 TCGA-CM-6675 
       14.99        12.99        13.02        15.02        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6532 
       11.08        10.06        12.03        13.51        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-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
       15.58        12.43        14.30         9.44         1.51        12.00 
TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       11.38        38.20        92.75        49.91        13.32       140.38 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G 
       44.32       135.65         7.76        26.47        81.37        60.79 
TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       98.24        11.11        13.64        35.87        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6298 
       16.24         1.28         0.53        19.43         8.35        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       74.56        43.07        61.87        53.62        44.68        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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2691 
        5.06         2.79         5.98        14.76        17.95        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6136 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       13.55        12.72        15.39        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 
        7.07         2.01        24.00         2.01         6.05         0.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 
        0.99        32.98        19.99         1.02        13.02        35.01 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A014 
       32.02        28.04         0.99        20.98        13.94        15.95 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 
        1.02        31.00        70.03        64.01        10.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-CI-6620 TCGA-CI-6624 
        1.94        38.96        61.97         1.45         6.05         4.73 
TCGA-CL-5918 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
        7.99         7.10        30.05        10.06         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6511 
       57.24        24.13        32.61         2.40        19.96        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       17.69        16.34        16.41         8.61        17.46         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6864 
       31.30        14.86         0.46 

  AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE 
                         15.995                          21.010 
[1] "0.1 - 139.2 (16.0)" "0.1 - 140.4 (21.0)"
[1] "hr=" "1.1"
D22V2, continuous
D22V3, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20P11.23) MUTATED   213  96
  AMP PEAK 22(20P11.23) WILD-TYPE 216  63
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20P11.23) MUTATED    213   96
  AMP PEAK 22(20P11.23) WILD-TYPE  216   63
        clus
vv       AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE
  COLON                            213                             216
  RECTUM                            96                              63
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 22(20P11.23) MUTATED        52        1       11        79         5
  AMP PEAK 22(20P11.23) WILD-TYPE      50        0       25        86         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(20P11.23) MUTATED           2        12         18         34
  AMP PEAK 22(20P11.23) WILD-TYPE         1        14          4         42
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 22(20P11.23) MUTATED           27       44        16         0
  AMP PEAK 22(20P11.23) WILD-TYPE         25       16         9         1
D22V4, multiclass
            clus
vv           AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE
  STAGE I                               52                              50
  STAGE IA                               1                               0
  STAGE II                              11                              25
  STAGE IIA                             79                              86
  STAGE IIB                              5                               5
  STAGE IIC                              2                               1
  STAGE III                             12                              14
  STAGE IIIA                            18                               4
  STAGE IIIB                            34                              42
  STAGE IIIC                            27                              25
  STAGE IV                              44                              16
  STAGE IVA                             16                               9
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 22(20P11.23) MUTATED      12  54 210  33
  AMP PEAK 22(20P11.23) WILD-TYPE     8  51 193  29
D22V5, multiclass
       clus
vv      AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE
  T0+T1                            12                               8
  T2                               54                              51
  T3                              210                             193
  T4                               33                              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 22(20P11.23) MUTATED   161  86  62
  AMP PEAK 22(20P11.23) WILD-TYPE 174  60  46
D22V6, multiclass
    clus
vv   AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE
  N0                           161                             174
  N1                            86                              60
  N2                            62                              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 22(20P11.23) MUTATED   215  48   9   0  35
  AMP PEAK 22(20P11.23) WILD-TYPE 228  24   0   1  23
D22V7, multiclass
     clus
vv    AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE
  M0                            215                             228
  M1                             48                              24
  M1A                             9                               0
  M1B                             0                               1
  MX                             35                              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"
D22V8, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20P11.23) MUTATED   134 177
  AMP PEAK 22(20P11.23) WILD-TYPE 143 138
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20P11.23) MUTATED    134  177
  AMP PEAK 22(20P11.23) WILD-TYPE  143  138
        clus
vv       AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE
  FEMALE                           134                             143
  MALE                             177                             138
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 22(20P11.23) MUTATED                    194
  AMP PEAK 22(20P11.23) WILD-TYPE                  179
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(20P11.23) MUTATED                              18
  AMP PEAK 22(20P11.23) WILD-TYPE                            37
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 22(20P11.23) MUTATED                      90
  AMP PEAK 22(20P11.23) WILD-TYPE                    53
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(20P11.23) MUTATED                                4
  AMP PEAK 22(20P11.23) WILD-TYPE                              9
D22V9, multiclass
                                clus
vv                               AMP PEAK 22(20P11.23) MUTATED
  COLON ADENOCARCINOMA                                     194
  COLON MUCINOUS ADENOCARCINOMA                             18
  RECTAL ADENOCARCINOMA                                     90
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               AMP PEAK 22(20P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                       179
  COLON MUCINOUS ADENOCARCINOMA                               37
  RECTAL ADENOCARCINOMA                                       53
  RECTAL MUCINOUS ADENOCARCINOMA                               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"
D22V10, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20P11.23) MUTATED     7 304
  AMP PEAK 22(20P11.23) WILD-TYPE   2 279
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20P11.23) MUTATED      7  304
  AMP PEAK 22(20P11.23) WILD-TYPE    2  279
     clus
vv    AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE
  NO                              7                               2
  YES                           304                             279
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 22(20P11.23) MUTATED   217   3  24  12
  AMP PEAK 22(20P11.23) WILD-TYPE 209   2  12  15
D22V11, multiclass
    clus
vv   AMP PEAK 22(20P11.23) MUTATED AMP PEAK 22(20P11.23) WILD-TYPE
  R0                           217                             209
  R1                             3                               2
  R2                            24                              12
  RX                            12                              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"
D22V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 22(20P11.23) MUTATED                                  1     7
  AMP PEAK 22(20P11.23) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(20P11.23) MUTATED                          21   159
  AMP PEAK 22(20P11.23) WILD-TYPE                        23   133
D22V13, multiclass
                                  clus
vv                                 AMP PEAK 22(20P11.23) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   21
  WHITE                                                      159
                                  clus
vv                                 AMP PEAK 22(20P11.23) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     23
  WHITE                                                        133
[1] 4 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(20P11.21) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(20P11.21) MUTATED   270  62
  AMP PEAK 23(20P11.21) WILD-TYPE 187  44
  AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE 
                            332                             231 
  AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE 
                             62                              44 
$`AMP PEAK 23(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-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
        1.41         5.13        83.80        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         3.19         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 
        2.14         3.29         0.07         0.26         1.35        17.56 
TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 
       40.34        48.20        21.99        20.02         8.02         8.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 
       13.02        29.06        22.03        22.98        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-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        13.02        15.02        14.04        11.01 
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-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       11.51        20.19        17.75        18.25         1.32         7.92 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6928 
       12.49         7.53        12.39        10.13         9.04        11.64 
TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D8 
       13.41        10.26       119.70        24.43       130.65        12.59 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E 
        7.50       131.51       139.17         6.12        14.04       119.93 
TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 
       35.97       117.07        95.18         8.61        13.38        13.45 
TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6293 
        6.18         1.55        33.67         1.28        35.41       107.67 
TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6306 
       28.21         8.35        82.39        23.51        61.87        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6322 
       55.04        45.11        39.42        35.93        36.72        26.04 
TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB 
       13.78        91.79        46.75        47.15         4.11         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 
       26.99        17.29        24.13        17.95        17.23        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       37.74        10.39         8.45        20.02        10.39        36.03 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
        8.02         7.07         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 
       12.03        15.95        19.99        19.99         7.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        14.04         1.02        17.03         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       64.01        51.98        41.00        38.04         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 
        0.72         4.60         1.81        10.19         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DG 
       12.95        13.05       126.44        41.36       129.27        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
        0.49        20.55        20.91        17.00        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       16.31        11.51        10.78        13.64        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       37.51        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`AMP PEAK 23(20P11.21) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-5657 
       46.65        23.38        42.28        37.05        37.25        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6141 
       33.53        23.61        22.09        22.06        32.71         8.38 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 
       20.61        21.76        24.39        23.87        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
       16.24        24.92        52.44         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
       63.98        13.02         1.02         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3543 
       36.03         8.05        19.07        34.03        26.01         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-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3678 TCGA-AA-3680 
       61.02         6.97        54.02         0.92        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3821 
        5.98        26.99        19.04         0.99        35.05         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 
       17.98        15.95        36.95        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       53.00        24.03        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
       26.01        24.00         2.01        25.02        27.02        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        30.02        34.03        18.05        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        34.98        32.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02R 
       35.01         1.02        35.01        37.02        39.06        22.03 
TCGA-AA-A03F TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 
       18.05         4.21        56.55         0.76         0.46         0.92 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 
       27.09        15.75        21.44        17.82        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 
       58.39         5.65        32.94        22.36        61.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
      100.01         5.23        11.74         3.25         0.33         0.10 
TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
      102.44        70.16        15.62        51.32        21.01         2.93 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
        2.01       124.27        23.05        37.02        26.04        27.02 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 
       30.08        15.02        12.00        14.99        12.99        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6535 
       13.05        11.08        12.03        13.51        20.42        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6923 
       17.85         4.50        17.13        16.14        15.58        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XF 
       14.30         9.44         1.51        12.00        11.38        38.20 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB 
       92.75        49.91        13.32       140.38        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 
        7.76        26.47        81.37        60.79        98.24        11.11 
TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6854 
       13.64        35.87        16.31        29.59        16.24         0.53 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6317 
       19.43        74.56        43.07        53.62        51.75        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A50V 
       26.43        22.09        35.80        26.17        52.80         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
        2.79         5.98        14.76        43.04        13.55        12.72 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3584 
       14.50        15.39        12.00        32.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3727 TCGA-AG-3732 
        1.02         2.01         6.05         0.99         0.99        32.98 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       13.02        35.01        28.04         0.99        20.98        13.94 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
        1.02        31.00        70.03        10.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-6158 
       38.96        61.97         1.45         6.05         4.73         7.10 
TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
       30.05        10.06         5.29        57.24        24.13        32.61 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
        2.40        19.96        15.85        16.34        16.41         8.61 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 
       17.46         8.45        31.30 

  AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE 
                         16.195                          21.440 
[1] "0.1 - 139.2 (16.2)" "0.1 - 140.4 (21.4)"
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20P11.21) MUTATED   239 108
  AMP PEAK 23(20P11.21) WILD-TYPE 190  51
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20P11.21) MUTATED    239  108
  AMP PEAK 23(20P11.21) WILD-TYPE  190   51
        clus
vv       AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE
  COLON                            239                             190
  RECTUM                           108                              51
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 23(20P11.21) MUTATED        62        1       16        91         5
  AMP PEAK 23(20P11.21) WILD-TYPE      40        0       20        74         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(20P11.21) MUTATED           2        11         18         39
  AMP PEAK 23(20P11.21) WILD-TYPE         1        15          4         37
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 23(20P11.21) MUTATED           30       47        17         0
  AMP PEAK 23(20P11.21) WILD-TYPE         22       13         8         1
D23V4, multiclass
            clus
vv           AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE
  STAGE I                               62                              40
  STAGE IA                               1                               0
  STAGE II                              16                              20
  STAGE IIA                             91                              74
  STAGE IIB                              5                               5
  STAGE IIC                              2                               1
  STAGE III                             11                              15
  STAGE IIIA                            18                               4
  STAGE IIIB                            39                              37
  STAGE IIIC                            30                              22
  STAGE IV                              47                              13
  STAGE IVA                             17                               8
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 23(20P11.21) MUTATED      13  65 234  35
  AMP PEAK 23(20P11.21) WILD-TYPE     7  40 169  27
D23V5, multiclass
       clus
vv      AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE
  T0+T1                            13                               7
  T2                               65                              40
  T3                              234                             169
  T4                               35                              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
  AMP PEAK 23(20P11.21) MUTATED   190  92  65
  AMP PEAK 23(20P11.21) WILD-TYPE 145  54  43
D23V6, multiclass
    clus
vv   AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE
  N0                           190                             145
  N1                            92                              54
  N2                            65                              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
  AMP PEAK 23(20P11.21) MUTATED   244  53   9   0  37
  AMP PEAK 23(20P11.21) WILD-TYPE 199  19   0   1  21
D23V7, multiclass
     clus
vv    AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE
  M0                            244                             199
  M1                             53                              19
  M1A                             9                               0
  M1B                             0                               1
  MX                             37                              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"
D23V8, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20P11.21) MUTATED   152 197
  AMP PEAK 23(20P11.21) WILD-TYPE 125 118
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20P11.21) MUTATED    152  197
  AMP PEAK 23(20P11.21) WILD-TYPE  125  118
        clus
vv       AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE
  FEMALE                           152                             125
  MALE                             197                             118
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 23(20P11.21) MUTATED                    218
  AMP PEAK 23(20P11.21) WILD-TYPE                  155
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(20P11.21) MUTATED                              20
  AMP PEAK 23(20P11.21) WILD-TYPE                            35
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 23(20P11.21) MUTATED                     103
  AMP PEAK 23(20P11.21) WILD-TYPE                    40
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(20P11.21) MUTATED                                4
  AMP PEAK 23(20P11.21) WILD-TYPE                              9
D23V9, multiclass
                                clus
vv                               AMP PEAK 23(20P11.21) MUTATED
  COLON ADENOCARCINOMA                                     218
  COLON MUCINOUS ADENOCARCINOMA                             20
  RECTAL ADENOCARCINOMA                                    103
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               AMP PEAK 23(20P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                       155
  COLON MUCINOUS ADENOCARCINOMA                               35
  RECTAL ADENOCARCINOMA                                       40
  RECTAL MUCINOUS ADENOCARCINOMA                               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"
D23V10, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20P11.21) MUTATED     7 342
  AMP PEAK 23(20P11.21) WILD-TYPE   2 241
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20P11.21) MUTATED      7  342
  AMP PEAK 23(20P11.21) WILD-TYPE    2  241
     clus
vv    AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE
  NO                              7                               2
  YES                           342                             241
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 23(20P11.21) MUTATED   248   3  25  14
  AMP PEAK 23(20P11.21) WILD-TYPE 178   2  11  13
D23V11, multiclass
    clus
vv   AMP PEAK 23(20P11.21) MUTATED AMP PEAK 23(20P11.21) WILD-TYPE
  R0                           248                             178
  R1                             3                               2
  R2                            25                              11
  RX                            14                              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"
D23V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 23(20P11.21) MUTATED                                  1     7
  AMP PEAK 23(20P11.21) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(20P11.21) MUTATED                          23   179
  AMP PEAK 23(20P11.21) WILD-TYPE                        21   113
D23V13, multiclass
                                  clus
vv                                 AMP PEAK 23(20P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   23
  WHITE                                                      179
                                  clus
vv                                 AMP PEAK 23(20P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     21
  WHITE                                                        113
[1] 4 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(20Q11.21) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 24(20Q11.21) MUTATED   349  80
  AMP PEAK 24(20Q11.21) WILD-TYPE 108  26
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                            429                             134 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                             80                              26 
$`AMP PEAK 24(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-AZ-4308 
        0.95        15.75         0.20         5.19         5.52        75.25 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41         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-F4-6806 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-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-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 
       23.51        61.87        44.68        55.04        45.11        39.42 
TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       35.93        36.72        36.00        26.43        26.04        13.78 
TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       91.79        46.75        47.15         4.11         5.06         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       26.99        17.29        24.13        17.95        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       20.02        10.39        36.03         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
        2.01        24.00         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98         1.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03         0.99        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         7.10        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       51.48        32.61         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       16.41        11.51        10.78        13.64        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

$`AMP PEAK 24(20Q11.21) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 TCGA-A6-5661 
       46.65        23.38        42.28        37.05        31.63        33.53 
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-3502 TCGA-AA-3510 TCGA-AA-3516 
       16.24        24.92         3.02        35.01        63.98        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
        1.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3680 
       29.95        61.02         6.97        54.02         0.92        11.01 
TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99        19.04         0.99         1.02        17.98        15.95 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       36.03        53.00        29.98        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A 
       26.01        24.00         2.01        25.02        27.02        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q 
       30.02        18.05         0.99        34.98        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 
       35.01        35.01        39.06        22.03        18.05        56.55 
TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 
        0.76         0.92        27.09        21.44        17.82        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       58.39         5.65        32.94        61.41         6.77       100.01 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 
       11.74         3.25         0.33         0.10        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 
       51.32        21.01         2.93       124.27        23.05        26.04 
TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 
       27.02        15.02        12.00        12.95        13.05        12.03 
TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 
       20.42        16.14        15.58         9.44         1.51        12.00 
TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K 
      140.38       135.65         7.76        81.37        60.79        98.24 
TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 
       11.11        35.87        16.31        19.43        74.56        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-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 
        2.79         5.98        14.76        13.55        12.72        12.00 
TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 
       32.02         2.01         6.05        32.98        13.02        20.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-CI-6620 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 
       49.97        61.97         6.05         5.29        19.96         8.61 
TCGA-EI-6917 TCGA-EI-7004 
       17.46         8.45 

  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                         17.030                          21.225 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (21.2)"
[1] "hr=" "1.1"
D24V2, continuous
D24V3, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20Q11.21) MUTATED   306 141
  AMP PEAK 24(20Q11.21) WILD-TYPE 123  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED    306  141
  AMP PEAK 24(20Q11.21) WILD-TYPE  123   18
        clus
vv       AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  COLON                            306                             123
  RECTUM                           141                              18
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 24(20Q11.21) MUTATED        77        1       21       113         5
  AMP PEAK 24(20Q11.21) WILD-TYPE      25        0       15        52         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(20Q11.21) MUTATED           3        19         21         60
  AMP PEAK 24(20Q11.21) WILD-TYPE         0         7          1         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 24(20Q11.21) MUTATED           43       54        22         0
  AMP PEAK 24(20Q11.21) WILD-TYPE          9        6         3         1
D24V4, multiclass
            clus
vv           AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  STAGE I                               77                              25
  STAGE IA                               1                               0
  STAGE II                              21                              15
  STAGE IIA                            113                              52
  STAGE IIB                              5                               5
  STAGE IIC                              3                               0
  STAGE III                             19                               7
  STAGE IIIA                            21                               1
  STAGE IIIB                            60                              16
  STAGE IIIC                            43                               9
  STAGE IV                              54                               6
  STAGE IVA                             22                               3
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 24(20Q11.21) MUTATED      14  84 308  42
  AMP PEAK 24(20Q11.21) WILD-TYPE     6  21  95  20
D24V5, multiclass
       clus
vv      AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  T0+T1                            14                               6
  T2                               84                              21
  T3                              308                              95
  T4                               42                              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 24(20Q11.21) MUTATED   236 124  87
  AMP PEAK 24(20Q11.21) WILD-TYPE  99  22  21
D24V6, multiclass
    clus
vv   AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  N0                           236                              99
  N1                           124                              22
  N2                            87                              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 24(20Q11.21) MUTATED   326  64   9   0  45
  AMP PEAK 24(20Q11.21) WILD-TYPE 117   8   0   1  13
D24V7, multiclass
     clus
vv    AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  M0                            326                             117
  M1                             64                               8
  M1A                             9                               0
  M1B                             0                               1
  MX                             45                              13
[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"
D24V8, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20Q11.21) MUTATED   205 245
  AMP PEAK 24(20Q11.21) WILD-TYPE  72  70
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED    205  245
  AMP PEAK 24(20Q11.21) WILD-TYPE   72   70
        clus
vv       AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  FEMALE                           205                              72
  MALE                             245                              70
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 24(20Q11.21) MUTATED                    281
  AMP PEAK 24(20Q11.21) WILD-TYPE                   92
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(20Q11.21) MUTATED                              24
  AMP PEAK 24(20Q11.21) WILD-TYPE                            31
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 24(20Q11.21) MUTATED                     132
  AMP PEAK 24(20Q11.21) WILD-TYPE                    11
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(20Q11.21) MUTATED                                7
  AMP PEAK 24(20Q11.21) WILD-TYPE                              6
D24V9, multiclass
                                clus
vv                               AMP PEAK 24(20Q11.21) MUTATED
  COLON ADENOCARCINOMA                                     281
  COLON MUCINOUS ADENOCARCINOMA                             24
  RECTAL ADENOCARCINOMA                                    132
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 24(20Q11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                        92
  COLON MUCINOUS ADENOCARCINOMA                               31
  RECTAL ADENOCARCINOMA                                       11
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20Q11.21) MUTATED     8 442
  AMP PEAK 24(20Q11.21) WILD-TYPE   1 141
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q11.21) MUTATED      8  442
  AMP PEAK 24(20Q11.21) WILD-TYPE    1  141
     clus
vv    AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  NO                              8                               1
  YES                           442                             141
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 24(20Q11.21) MUTATED   321   4  32  16
  AMP PEAK 24(20Q11.21) WILD-TYPE 105   1   4  11
D24V11, multiclass
    clus
vv   AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE
  R0                           321                             105
  R1                             4                               1
  R2                            32                               4
  RX                            16                              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"
D24V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 24(20Q11.21) MUTATED                                  1     7
  AMP PEAK 24(20Q11.21) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(20Q11.21) MUTATED                          31   228
  AMP PEAK 24(20Q11.21) WILD-TYPE                        13    64
D24V13, multiclass
                                  clus
vv                                 AMP PEAK 24(20Q11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      228
                                  clus
vv                                 AMP PEAK 24(20Q11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     13
  WHITE                                                         64
[1] 4 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(20Q12) MUTATION ANALYSIS
D25V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 25(20Q12) MUTATED   351  80
  AMP PEAK 25(20Q12) WILD-TYPE 106  26
  AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE 
                         431                          132 
  AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE 
                          80                           26 
$`AMP PEAK 25(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-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 
        0.20         5.19         5.52        75.25         1.41         5.65 
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-6607 TCGA-AZ-6608 TCGA-CA-5254 
       12.10        29.56         5.23         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-4948 TCGA-CK-4950 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
       17.56       102.44        40.34        48.20        21.99         2.01 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       20.02        37.02         8.02         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 
       22.03        22.98        30.08        16.01         5.03        15.02 
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-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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 
       11.01        11.08        11.08        11.01        10.06        14.99 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 
       12.26        19.59        13.51        11.51        20.19        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25         1.32         7.92        15.12        17.85         4.50 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       17.13        12.49         7.53        12.39        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 
       14.30         9.04        11.64        13.41        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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 
       13.32        12.59         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
        6.12        14.04        26.47       119.93        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        13.38        13.64        13.45         6.18 
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-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-G4-6307 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-G4-6322 
       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         5.06 
TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        5.59        26.99        17.29        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       43.04        19.10        37.74        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 
       15.39        20.02        10.39        36.03         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98         1.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03         0.99        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98         1.94        38.96        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

$`AMP PEAK 25(20Q12) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 TCGA-A6-5661 
       46.65        23.38        42.28        37.05        31.63        33.53 
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-3502 TCGA-AA-3510 TCGA-AA-3516 
       16.24        24.92         3.02        35.01        63.98        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
        1.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3680 
       29.95        61.02         6.97        54.02         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-A01D 
       38.04        30.02        18.05         0.99        34.98         0.99 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R 
       38.07         1.02        35.01        35.01        39.06        22.03 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
       18.05        56.55         0.76         0.92        27.09        21.44 
TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 
       17.82        50.37        58.39        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        21.01         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-F4-6856 TCGA-G4-6302 TCGA-G4-6304 
       98.24        11.11        35.87        19.43        43.07        53.62 
TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV 
       51.75        22.09        35.80        26.17        52.80         2.79 
TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 
        5.98        14.76        13.55        12.72        12.00        32.02 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A025 
        2.01         6.05        32.98        13.02        20.98        49.97 
TCGA-AG-A02N TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       61.97         5.29        19.96         8.61        17.46         8.45 

  AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE 
                        0.07                         0.10 
  AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE 
                      139.17                       140.38 
  AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE 
                      17.030                       21.225 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (21.2)"
[1] "hr=" "1.1"
D25V2, continuous
D25V3, binary
                              cls
clus                             0   1
  AMP PEAK 25(20Q12) MUTATED   307 142
  AMP PEAK 25(20Q12) WILD-TYPE 122  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(20Q12) MUTATED    307  142
  AMP PEAK 25(20Q12) WILD-TYPE  122   17
        clus
vv       AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE
  COLON                         307                          122
  RECTUM                        142                           17
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 25(20Q12) MUTATED        77        1       21       114         5
  AMP PEAK 25(20Q12) WILD-TYPE      25        0       15        51         5
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 25(20Q12) MUTATED           3        18         21         60
  AMP PEAK 25(20Q12) WILD-TYPE         0         8          1         16
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 25(20Q12) MUTATED           43       54        24         0
  AMP PEAK 25(20Q12) WILD-TYPE          9        6         1         1
D25V4, multiclass
            clus
vv           AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE
  STAGE I                            77                           25
  STAGE IA                            1                            0
  STAGE II                           21                           15
  STAGE IIA                         114                           51
  STAGE IIB                           5                            5
  STAGE IIC                           3                            0
  STAGE III                          18                            8
  STAGE IIIA                         21                            1
  STAGE IIIB                         60                           16
  STAGE IIIC                         43                            9
  STAGE IV                           54                            6
  STAGE IVA                          24                            1
  STAGE IVB                           0                            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                           T0+T1  T2  T3  T4
  AMP PEAK 25(20Q12) MUTATED      14  84 309  43
  AMP PEAK 25(20Q12) WILD-TYPE     6  21  94  19
D25V5, multiclass
       clus
vv      AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE
  T0+T1                         14                            6
  T2                            84                           21
  T3                           309                           94
  T4                            43                           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 25(20Q12) MUTATED   237 125  87
  AMP PEAK 25(20Q12) WILD-TYPE  98  21  21
D25V6, multiclass
    clus
vv   AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE
  N0                        237                           98
  N1                        125                           21
  N2                         87                           21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B  MX
  AMP PEAK 25(20Q12) MUTATED   326  66   9   0  45
  AMP PEAK 25(20Q12) WILD-TYPE 117   6   0   1  13
D25V7, multiclass
     clus
vv    AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE
  M0                         326                          117
  M1                          66                            6
  M1A                          9                            0
  M1B                          0                            1
  MX                          45                           13
[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"
D25V8, binary
                              cls
clus                             0   1
  AMP PEAK 25(20Q12) MUTATED   206 246
  AMP PEAK 25(20Q12) WILD-TYPE  71  69
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(20Q12) MUTATED    206  246
  AMP PEAK 25(20Q12) WILD-TYPE   71   69
        clus
vv       AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE
  FEMALE                        206                           71
  MALE                          246                           69
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 25(20Q12) MUTATED                    283
  AMP PEAK 25(20Q12) WILD-TYPE                   90
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 25(20Q12) MUTATED                              23
  AMP PEAK 25(20Q12) WILD-TYPE                            32
                              vv
clus                           RECTAL ADENOCARCINOMA
  AMP PEAK 25(20Q12) MUTATED                     133
  AMP PEAK 25(20Q12) WILD-TYPE                    10
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 25(20Q12) MUTATED                                7
  AMP PEAK 25(20Q12) WILD-TYPE                              6
D25V9, multiclass
                                clus
vv                               AMP PEAK 25(20Q12) MUTATED
  COLON ADENOCARCINOMA                                  283
  COLON MUCINOUS ADENOCARCINOMA                          23
  RECTAL ADENOCARCINOMA                                 133
  RECTAL MUCINOUS ADENOCARCINOMA                          7
                                clus
vv                               AMP PEAK 25(20Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                     90
  COLON MUCINOUS ADENOCARCINOMA                            32
  RECTAL ADENOCARCINOMA                                    10
  RECTAL MUCINOUS ADENOCARCINOMA                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                              cls
clus                             0   1
  AMP PEAK 25(20Q12) MUTATED     8 444
  AMP PEAK 25(20Q12) WILD-TYPE   1 139
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 25(20Q12) MUTATED      8  444
  AMP PEAK 25(20Q12) WILD-TYPE    1  139
     clus
vv    AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE
  NO                           8                            1
  YES                        444                          139
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 25(20Q12) MUTATED   322   4  32  16
  AMP PEAK 25(20Q12) WILD-TYPE 104   1   4  11
D25V11, multiclass
    clus
vv   AMP PEAK 25(20Q12) MUTATED AMP PEAK 25(20Q12) WILD-TYPE
  R0                        322                          104
  R1                          4                            1
  R2                         32                            4
  RX                         16                           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"
D25V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 25(20Q12) MUTATED                                  1     7
  AMP PEAK 25(20Q12) WILD-TYPE                                0     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(20Q12) MUTATED                          31   232
  AMP PEAK 25(20Q12) WILD-TYPE                        13    60
D25V13, multiclass
                                  clus
vv                                 AMP PEAK 25(20Q12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          1
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                31
  WHITE                                                   232
                                  clus
vv                                 AMP PEAK 25(20Q12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                      60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = AMP PEAK 26(20Q13.31) MUTATION ANALYSIS
D26V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 26(20Q13.31) MUTATED   353  81
  AMP PEAK 26(20Q13.31) WILD-TYPE 104  25
  AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE 
                            434                             129 
  AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE 
                             81                              25 
$`AMP PEAK 26(20Q13.31) 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-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 
       15.02         5.98        37.05        19.00        36.00         5.03 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 
       85.05         0.99        35.05         0.99        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-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 
       32.05         0.99        31.07        31.07        17.03        24.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       27.02        18.05        12.99        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
        2.01        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-A004 
       26.01        24.00        27.02        19.07         7.96        13.94 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O 
       19.00        34.03        18.05        17.03         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       42.02        17.03        14.99        21.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S 
        0.99        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       33.04        26.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J 
        2.01         5.03         0.92        41.00        39.98        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 
        0.07        21.37         4.21         0.79         0.72         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
        1.02         0.10         0.43         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
        0.95        15.75         0.20         5.19         5.52        75.25 
TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41         5.13        83.80        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41        12.10        29.56         5.23        11.74         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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6294 
       33.67         1.28         0.53        35.41       107.67        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
        8.35        82.39        23.51        74.56        61.87        44.68 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       55.04        45.11        39.42        35.93        36.72        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 
       26.43        26.04        13.78        91.79        46.75        47.15 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2687 
        4.11         5.06         5.59        26.99        17.29        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        43.04        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        13.64        11.97         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`AMP PEAK 26(20Q13.31) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5657 TCGA-A6-5661 
       46.65        23.38        42.28        37.05        31.63        33.53 
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-3502 TCGA-AA-3510 TCGA-AA-3516 
       16.24        24.92         3.02        35.01        63.98        13.02 
TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
        1.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3710 
       29.95        61.02         6.97         0.92        11.01        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3854 
       19.04         0.99         1.02        17.98        15.95        36.03 
TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       53.00        29.98        31.00         2.01        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E 
       24.00         2.01        25.02        27.02        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       18.05         0.99        34.98        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A024 TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6964 
       35.01        39.06        22.03        18.05        56.55         0.76 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 
        0.20         0.92        27.09        21.44        17.82        50.37 
TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 
       58.39         5.65        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 
       21.01         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-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 
       35.80        26.17        52.80         2.79         5.98        14.76 
TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 
       12.72        12.00        32.02         2.01         6.05        32.98 
TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-DT-5265 TCGA-EI-6507 
       13.02        20.98        49.97        61.97         5.29        19.96 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
        8.61        17.46         8.45 

  AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE 
                           0.07                            0.10 
  AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE 
                         139.17                          140.38 
  AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE 
                          17.03                           21.44 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (21.4)"
[1] "hr=" "1.1"
D26V2, continuous
D26V3, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20Q13.31) MUTATED   309 142
  AMP PEAK 26(20Q13.31) WILD-TYPE 120  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.31) MUTATED    309  142
  AMP PEAK 26(20Q13.31) WILD-TYPE  120   17
        clus
vv       AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE
  COLON                            309                             120
  RECTUM                           142                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 26(20Q13.31) MUTATED        77        1       22       115         5
  AMP PEAK 26(20Q13.31) WILD-TYPE      25        0       14        50         5
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 26(20Q13.31) MUTATED           3        19         21         60
  AMP PEAK 26(20Q13.31) WILD-TYPE         0         7          1         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 26(20Q13.31) MUTATED           44       55        23         0
  AMP PEAK 26(20Q13.31) WILD-TYPE          8        5         2         1
D26V4, multiclass
            clus
vv           AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE
  STAGE I                               77                              25
  STAGE IA                               1                               0
  STAGE II                              22                              14
  STAGE IIA                            115                              50
  STAGE IIB                              5                               5
  STAGE IIC                              3                               0
  STAGE III                             19                               7
  STAGE IIIA                            21                               1
  STAGE IIIB                            60                              16
  STAGE IIIC                            44                               8
  STAGE IV                              55                               5
  STAGE IVA                             23                               2
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  AMP PEAK 26(20Q13.31) MUTATED      14  84 313  42
  AMP PEAK 26(20Q13.31) WILD-TYPE     6  21  90  20
D26V5, multiclass
       clus
vv      AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE
  T0+T1                            14                               6
  T2                               84                              21
  T3                              313                              90
  T4                               42                              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 26(20Q13.31) MUTATED   239 125  88
  AMP PEAK 26(20Q13.31) WILD-TYPE  96  21  20
D26V6, multiclass
    clus
vv   AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE
  N0                           239                              96
  N1                           125                              21
  N2                            88                              20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  AMP PEAK 26(20Q13.31) MUTATED   330  66   9   0  44
  AMP PEAK 26(20Q13.31) WILD-TYPE 113   6   0   1  14
D26V7, multiclass
     clus
vv    AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE
  M0                            330                             113
  M1                             66                               6
  M1A                             9                               0
  M1B                             0                               1
  MX                             44                              14
[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"
D26V8, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20Q13.31) MUTATED   209 246
  AMP PEAK 26(20Q13.31) WILD-TYPE  68  69
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.31) MUTATED    209  246
  AMP PEAK 26(20Q13.31) WILD-TYPE   68   69
        clus
vv       AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE
  FEMALE                           209                              68
  MALE                             246                              69
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 26(20Q13.31) MUTATED                    284
  AMP PEAK 26(20Q13.31) WILD-TYPE                   89
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 26(20Q13.31) MUTATED                              24
  AMP PEAK 26(20Q13.31) WILD-TYPE                            31
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 26(20Q13.31) MUTATED                     133
  AMP PEAK 26(20Q13.31) WILD-TYPE                    10
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 26(20Q13.31) MUTATED                                7
  AMP PEAK 26(20Q13.31) WILD-TYPE                              6
D26V9, multiclass
                                clus
vv                               AMP PEAK 26(20Q13.31) MUTATED
  COLON ADENOCARCINOMA                                     284
  COLON MUCINOUS ADENOCARCINOMA                             24
  RECTAL ADENOCARCINOMA                                    133
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 26(20Q13.31) WILD-TYPE
  COLON ADENOCARCINOMA                                        89
  COLON MUCINOUS ADENOCARCINOMA                               31
  RECTAL ADENOCARCINOMA                                       10
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, binary
                                 cls
clus                                0   1
  AMP PEAK 26(20Q13.31) MUTATED     8 447
  AMP PEAK 26(20Q13.31) WILD-TYPE   1 136
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 26(20Q13.31) MUTATED      8  447
  AMP PEAK 26(20Q13.31) WILD-TYPE    1  136
     clus
vv    AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE
  NO                              8                               1
  YES                           447                             136
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 26(20Q13.31) MUTATED   325   4  32  16
  AMP PEAK 26(20Q13.31) WILD-TYPE 101   1   4  11
D26V11, multiclass
    clus
vv   AMP PEAK 26(20Q13.31) MUTATED AMP PEAK 26(20Q13.31) WILD-TYPE
  R0                           325                             101
  R1                             4                               1
  R2                            32                               4
  RX                            16                              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"
D26V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 26(20Q13.31) MUTATED                                  1     7
  AMP PEAK 26(20Q13.31) WILD-TYPE                                0     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 26(20Q13.31) MUTATED                          31   232
  AMP PEAK 26(20Q13.31) WILD-TYPE                        13    60
D26V13, multiclass
                                  clus
vv                                 AMP PEAK 26(20Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        7
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      232
                                  clus
vv                                 AMP PEAK 26(20Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     13
  WHITE                                                         60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = AMP PEAK 27(XQ28) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 27(XQ28) MUTATED    81  29
  AMP PEAK 27(XQ28) WILD-TYPE 376  77
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                        110                         453 
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                         29                          77 
$`AMP PEAK 27(XQ28) MUTATED`
TCGA-3L-AA1B TCGA-A6-2681 TCGA-A6-2686 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 
        5.06        45.60        16.04        24.16        20.61        24.69 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3524 
       23.87        52.44        37.05        35.01        58.03        36.03 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3558 TCGA-AA-3562 TCGA-AA-3660 
       29.00        12.99        14.01        20.98        19.99        78.08 
TCGA-AA-3664 TCGA-AA-3679 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3812 
       54.02        15.02         5.03        85.05         0.99        35.05 
TCGA-AA-3818 TCGA-AA-3860 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-A004 TCGA-AA-A00D 
        0.99        31.07        27.02        24.00        13.94        19.00 
TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02Y TCGA-AD-6888 
       32.02        33.04        51.98         0.92        39.98         4.21 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4323 
        0.20         0.43        16.31         0.20         5.19         1.41 
TCGA-AZ-4614 TCGA-AZ-6598 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 
        5.65        49.41       100.01        11.74         3.19         1.94 
TCGA-CA-6719 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6161 
        1.35        22.98        16.01         5.03        15.02        15.02 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 TCGA-D5-5539 TCGA-D5-6537 TCGA-D5-6538 
       21.99        14.99        13.05        19.59         4.50        17.13 
TCGA-D5-6923 TCGA-D5-6931 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1DA TCGA-DM-A285 
       12.43        12.00       119.70        24.43         7.50         6.12 
TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6570 TCGA-G4-6299 TCGA-G4-6303 
       35.97        95.18        13.38         6.18        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6311 TCGA-NH-A6GB TCGA-AF-2692 
       44.68        55.04        45.11        39.42         5.59        13.55 
TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3584 TCGA-AG-3587 
       19.10        10.39         8.45        12.00        24.00        46.03 
TCGA-AG-3594 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3893 TCGA-AG-4007 
        2.01        19.99        19.99         7.99        35.01         1.02 
TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A02X TCGA-AH-6644 
        0.99        15.95        36.03         9.07        41.00         0.72 
TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6156 TCGA-DY-A1DD 
        9.37        60.03        10.98        12.00        15.02        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6510 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 
      129.27        24.13        18.28        13.64         9.96        37.51 
TCGA-F5-6810 TCGA-F5-6863 
        0.39         0.76 

$`AMP PEAK 27(XQ28) 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-A6-2680 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-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        36.53        14.53        32.45        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-A6-6651 TCGA-A6-6653 TCGA-A6-6780 
        8.38        25.08        25.18        21.76        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-3496 TCGA-AA-3510 
        5.03         1.02         3.02         1.02         1.02        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-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-3538 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 
       29.00        26.01         0.99        33.99        21.01        13.02 
TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 
       24.00        17.95        29.95        23.01        19.99        13.94 
TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
       61.02         6.05         6.97         2.01        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-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3819 
       19.00        36.00        26.99        19.04         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-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
        0.99        31.07        53.00        17.03        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        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-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-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-A01G TCGA-AA-A01I 
       34.98        15.02        15.02         0.99        12.00        31.00 
TCGA-AA-A01K 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-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       26.01        37.02        39.06         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        5.03        22.03        41.00        18.05        40.96         0.07 
TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6899 TCGA-AD-6901 
       21.37        56.55         0.79         0.72         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.10         0.76         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AZ-4308 
        0.95        15.75        21.44        17.82         5.52        75.25 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
       50.37        58.39        32.94         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        61.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        5.23         2.24         3.06         2.14         3.25         3.29 
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-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 
       21.01         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-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       29.06        22.03        30.08        15.02        15.02        17.03 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 
       12.00        14.04        29.03        16.04        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-D5-5540 
       11.01        10.06        12.03        14.99        12.26        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-D5-6534 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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        10.13        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XF 
       11.64        13.41         1.51        11.38        10.26        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-A288 
       44.32       131.51       135.65         7.76       139.17        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-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 
        8.61        11.11        13.64        13.45        35.87         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-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-G4-6298 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6314 TCGA-G4-6315 
       23.51        43.07        53.62        51.75        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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        5.06         2.79         5.98        26.99        17.29        14.76 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 
       24.13        17.95        17.23        43.04        12.72        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 
       14.50        15.39        20.02        10.39        36.03        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 
        8.02         7.07         1.02         2.01         1.02        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3727 
       50.04        12.03         6.05         0.99        15.95         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        17.03        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       37.02         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       38.04         0.49         1.45         0.69         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.05         6.97         4.73        13.97 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        7.99        11.01        15.02        12.99        13.97        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        7.10        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      126.44        41.36        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       17.46        11.97         8.45        31.30        14.86         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                       0.20                        0.07 
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                     129.27                      140.38 
  AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE 
                      16.72                       17.95 
[1] "0.2 - 129.3 (16.7)" "0.1 - 140.4 (17.9)"
[1] "hr=" "1.5"
D27V2, continuous
D27V3, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ28) MUTATED    83  35
  AMP PEAK 27(XQ28) WILD-TYPE 346 124
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ28) MUTATED     83   35
  AMP PEAK 27(XQ28) WILD-TYPE  346  124
        clus
vv       AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  COLON                         83                         346
  RECTUM                        35                         124
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 27(XQ28) MUTATED        22        0       10        23         0
  AMP PEAK 27(XQ28) WILD-TYPE      80        1       26       142        10
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 27(XQ28) MUTATED           0         5          2         20
  AMP PEAK 27(XQ28) WILD-TYPE         3        21         20         56
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 27(XQ28) MUTATED           14       14         7         1
  AMP PEAK 27(XQ28) WILD-TYPE         38       46        18         0
D27V4, multiclass
            clus
vv           AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  STAGE I                           22                          80
  STAGE IA                           0                           1
  STAGE II                          10                          26
  STAGE IIA                         23                         142
  STAGE IIB                          0                          10
  STAGE IIC                          0                           3
  STAGE III                          5                          21
  STAGE IIIA                         2                          20
  STAGE IIIB                        20                          56
  STAGE IIIC                        14                          38
  STAGE IV                          14                          46
  STAGE IVA                          7                          18
  STAGE IVB                          1                           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                          T0+T1  T2  T3  T4
  AMP PEAK 27(XQ28) MUTATED       2  24  79  15
  AMP PEAK 27(XQ28) WILD-TYPE    18  81 324  47
D27V5, multiclass
       clus
vv      AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  T0+T1                         2                          18
  T2                           24                          81
  T3                           79                         324
  T4                           15                          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
  AMP PEAK 27(XQ28) MUTATED    58  29  31
  AMP PEAK 27(XQ28) WILD-TYPE 277 117  77
D27V6, multiclass
    clus
vv   AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  N0                        58                         277
  N1                        29                         117
  N2                        31                          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
  AMP PEAK 27(XQ28) MUTATED    88  17   3   1  10
  AMP PEAK 27(XQ28) WILD-TYPE 355  55   6   0  48
D27V7, multiclass
     clus
vv    AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  M0                         88                         355
  M1                         17                          55
  M1A                         3                           6
  M1B                         1                           0
  MX                         10                          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"
D27V8, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ28) MUTATED    54  66
  AMP PEAK 27(XQ28) WILD-TYPE 223 249
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ28) MUTATED     54   66
  AMP PEAK 27(XQ28) WILD-TYPE  223  249
        clus
vv       AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  FEMALE                        54                         223
  MALE                          66                         249
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  AMP PEAK 27(XQ28) MUTATED                     79
  AMP PEAK 27(XQ28) WILD-TYPE                  294
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 27(XQ28) MUTATED                               4
  AMP PEAK 27(XQ28) WILD-TYPE                            51
                             vv
clus                          RECTAL ADENOCARCINOMA
  AMP PEAK 27(XQ28) MUTATED                      33
  AMP PEAK 27(XQ28) WILD-TYPE                   110
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 27(XQ28) MUTATED                                1
  AMP PEAK 27(XQ28) WILD-TYPE                             12
D27V9, multiclass
                                clus
vv                               AMP PEAK 27(XQ28) MUTATED
  COLON ADENOCARCINOMA                                  79
  COLON MUCINOUS ADENOCARCINOMA                          4
  RECTAL ADENOCARCINOMA                                 33
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               AMP PEAK 27(XQ28) WILD-TYPE
  COLON ADENOCARCINOMA                                   294
  COLON MUCINOUS ADENOCARCINOMA                           51
  RECTAL ADENOCARCINOMA                                  110
  RECTAL MUCINOUS ADENOCARCINOMA                          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"
D27V10, binary
                             cls
clus                            0   1
  AMP PEAK 27(XQ28) MUTATED     1 119
  AMP PEAK 27(XQ28) WILD-TYPE   8 464
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 27(XQ28) MUTATED      1  119
  AMP PEAK 27(XQ28) WILD-TYPE    8  464
     clus
vv    AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  NO                          1                           8
  YES                       119                         464
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK 27(XQ28) MUTATED    84   1   9   2
  AMP PEAK 27(XQ28) WILD-TYPE 342   4  27  25
D27V11, multiclass
    clus
vv   AMP PEAK 27(XQ28) MUTATED AMP PEAK 27(XQ28) WILD-TYPE
  R0                        84                         342
  R1                         1                           4
  R2                         9                          27
  RX                         2                          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"
D27V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 27(XQ28) MUTATED                                  0     1
  AMP PEAK 27(XQ28) WILD-TYPE                                1    11
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 27(XQ28) MUTATED                          11    57
  AMP PEAK 27(XQ28) WILD-TYPE                        33   235
D27V13, multiclass
                                  clus
vv                                 AMP PEAK 27(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                               11
  WHITE                                                   57
                                  clus
vv                                 AMP PEAK 27(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     11
  BLACK OR AFRICAN AMERICAN                                 33
  WHITE                                                    235
[1] 4 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  1(1P36.11) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   176  48
  DEL PEAK  1(1P36.11) WILD-TYPE 281  58
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           224                            339 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            48                             58 
$`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-A6GA TCGA-QG-A5YV 
       36.00        91.79        46.75         4.11         5.98        26.99 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 
       24.13        17.23        43.04        13.55        19.10        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       14.50        15.39        32.02         1.02         2.01        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 
       46.03        34.03         6.05        19.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 
        1.02        19.99         1.02        36.95        17.03         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00H 
       48.03        19.99        28.04        36.03        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 
       23.01        12.00        70.03        64.01        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 
       38.96        38.04         0.49         0.69         0.72        10.19 
TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        6.97         4.73        11.01        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA 
       15.02        36.00        30.05        12.95        10.06       126.44 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6511 
      129.27        32.61         0.49         2.40        20.55        15.85 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 
       11.97         8.45        14.86         1.02         0.69         0.46 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
        5.06        37.02        46.65        43.43        23.38        42.28 
TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-5656 
       45.60        37.05        37.25        16.04        34.65        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       31.63        30.44        33.53        22.09        22.06        27.09 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        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-3532 TCGA-AA-3534 
        1.02        24.03        36.03         8.05        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 
       26.01        12.99         0.99        33.99        21.01        17.95 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       29.95        20.98        19.99        13.94        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
        6.05         6.97        54.02         0.92        47.05        15.02 
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-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3844 
       35.05         0.99         1.02        17.98        15.95        14.93 
TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       17.03        36.03        53.00        27.02        18.05        31.00 
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-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 
       16.08        34.06        25.02        24.00        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-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-A01D TCGA-AA-A01G TCGA-AA-A01I 
       14.99        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-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.06        51.98         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 
        0.07        21.37         4.21        56.55         0.72         0.10 
TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.76         0.92        27.09         0.95        15.75         0.20 
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-4615 TCGA-AZ-4681 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        1.41        32.94        83.80        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5796 TCGA-CA-6717 
        6.77       100.01        11.74         1.94         3.25         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-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       48.20        51.32        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 
       20.02        37.02        26.04        27.02        29.06        22.98 
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-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-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       13.05        11.08        11.01        12.26        19.59        11.51 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       20.42        18.25         4.50        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
        7.53        12.39        10.13         9.04         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-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA 
      130.65        13.32        12.59       140.38         7.50       131.51 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      135.65         7.76        14.04        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       60.79        98.24         8.61        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6856 
       35.87        16.31        16.24        33.67         0.53        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
      107.67        28.21        74.56        43.07        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6321 
       55.04        51.75        45.11        39.42        26.43        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-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 
        5.06         2.79         5.59        17.29        14.76        17.95 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       12.72        37.74         8.45        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
       12.00         8.02         7.07         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3732 
       12.03         0.99        15.95        19.99         7.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 
        0.99         0.99        13.02        35.01        14.01        32.02 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02        17.03         0.99        20.98         6.02 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 
       10.98        49.97        61.97        41.00         1.45         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        1.81         6.05         6.05         9.37        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 
        7.99        10.98        15.02         7.10        13.05         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6507 TCGA-EI-6508 
       41.36        57.24        24.13        51.48        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       17.00        18.28        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 
        8.61        11.51        10.78        13.64        17.46         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       37.51        31.30         0.39         0.66         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.76        18.28        55.76 

  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 
                         17.03                          18.05 
[1] "0.1 - 139.2 (17.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.4"
D28V2, continuous
D28V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   161  70
  DEL PEAK  1(1P36.11) WILD-TYPE 268  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    161   70
  DEL PEAK  1(1P36.11) WILD-TYPE  268   89
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  COLON                           161                            268
  RECTUM                           70                             89
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  1(1P36.11) MUTATED        33        0        8        59         3
  DEL PEAK  1(1P36.11) WILD-TYPE      69        1       28       106         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED           1        10          8         29
  DEL PEAK  1(1P36.11) WILD-TYPE         2        16         14         47
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.11) MUTATED           25       36        15         0
  DEL PEAK  1(1P36.11) WILD-TYPE         27       24        10         1
D28V4, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              33                             69
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            59                            106
  STAGE IIB                             3                              7
  STAGE IIC                             1                              2
  STAGE III                            10                             16
  STAGE IIIA                            8                             14
  STAGE IIIB                           29                             47
  STAGE IIIC                           25                             27
  STAGE IV                             36                             24
  STAGE IVA                            15                             10
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED       5  40 159  29
  DEL PEAK  1(1P36.11) WILD-TYPE    15  65 244  33
D28V5, multiclass
       clus
vv      DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T0+T1                            5                             15
  T2                              40                             65
  T3                             159                            244
  T4                              29                             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  1(1P36.11) MUTATED   113  64  55
  DEL PEAK  1(1P36.11) WILD-TYPE 222  82  53
D28V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                          113                            222
  N1                           64                             82
  N2                           55                             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  1(1P36.11) MUTATED   157  45   5   0  24
  DEL PEAK  1(1P36.11) WILD-TYPE 286  27   4   1  34
D28V7, multiclass
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                           157                            286
  M1                            45                             27
  M1A                            5                              4
  M1B                            0                              1
  MX                            24                             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"
D28V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   102 132
  DEL PEAK  1(1P36.11) WILD-TYPE 175 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    102  132
  DEL PEAK  1(1P36.11) WILD-TYPE  175  183
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                          102                            175
  MALE                            132                            183
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                    150
  DEL PEAK  1(1P36.11) WILD-TYPE                  223
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                              10
  DEL PEAK  1(1P36.11) WILD-TYPE                            45
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                      62
  DEL PEAK  1(1P36.11) WILD-TYPE                    81
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                                7
  DEL PEAK  1(1P36.11) WILD-TYPE                              6
D28V9, multiclass
                                clus
vv                               DEL PEAK  1(1P36.11) MUTATED
  COLON ADENOCARCINOMA                                    150
  COLON MUCINOUS ADENOCARCINOMA                            10
  RECTAL ADENOCARCINOMA                                    62
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK  1(1P36.11) WILD-TYPE
  COLON ADENOCARCINOMA                                      223
  COLON MUCINOUS ADENOCARCINOMA                              45
  RECTAL ADENOCARCINOMA                                      81
  RECTAL MUCINOUS ADENOCARCINOMA                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     4 230
  DEL PEAK  1(1P36.11) WILD-TYPE   5 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      4  230
  DEL PEAK  1(1P36.11) WILD-TYPE    5  353
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             4                              5
  YES                          230                            353
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   158   2  21  11
  DEL PEAK  1(1P36.11) WILD-TYPE 268   3  15  16
D28V11, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          158                            268
  R1                            2                              3
  R2                           21                             15
  RX                           11                             16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V12, 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     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED                          16   115
  DEL PEAK  1(1P36.11) WILD-TYPE                        28   177
D28V13, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.11) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  16
  WHITE                                                     115
                                  clus
vv                                 DEL PEAK  1(1P36.11) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    28
  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(29) Variable = DEL PEAK  2(1P33) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1P33) MUTATED   122  37
  DEL PEAK  2(1P33) WILD-TYPE 335  69
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        159                         404 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         37                          69 
$`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-A6GA TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2690 
       46.75         4.11         5.98        26.99        24.13        17.23 
TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 
       13.55        14.50        15.39        32.02         1.02        24.00 
TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 
       34.03        29.98         1.02        19.99         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       19.99        28.04        36.03        25.97        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       70.03         1.94        38.96        38.04         0.49         0.69 
TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 
       10.19         9.37         4.73        13.97        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE 
       12.99        13.97        36.00        30.05       126.44       129.27 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6702 
        0.49        20.55        15.85        13.64        11.97        14.86 
TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6572 
        1.02         0.69        47.08 

$`DEL PEAK  2(1P33) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        37.02        46.65        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-3807 
       42.28        44.91        45.60        13.94        37.05        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-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       32.71        27.09        24.13         8.38        25.08        25.18 
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-A6-6782 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-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-3520 TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 
       24.03        36.03        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-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-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       19.99        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 
       54.02         2.01        14.01         0.92        47.05        47.01 
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-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3856 
       17.98        15.95        14.93        17.03        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        27.02        29.98        18.05        31.00 
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-3972 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 
       34.03        16.08        50.99        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-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02         0.99        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-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       39.98         5.03         0.92        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6963 
        0.07        21.37         4.21        56.55         0.72         0.10 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
        0.76         0.46         0.92        27.09         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
        0.20        21.44        17.82         5.19        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41        32.94        83.80        22.36        65.00 
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-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-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-6751 TCGA-CM-4743 
       51.32        21.99        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 
       20.02        37.02         8.02        26.04        27.02        29.06 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       22.98        30.08        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-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-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       14.99        12.26        19.59        11.51        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       17.75        18.25         7.92         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-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      119.70        24.43       130.65        13.32        12.59       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-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-F4-6459 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-F4-6805 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-F4-6856 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-QG-A5YX 
       47.15        52.80         5.06         2.79         5.59        17.29 
TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       14.76        17.95        43.04        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       10.39         8.45        20.02        10.39        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
        8.02         7.07         2.01         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       32.02        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       13.94         6.02        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        31.00        64.01        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       61.97        41.00         1.45         0.72         4.60         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        6.05         6.05         6.97        60.03         7.99        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       12.00        15.02         7.10        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
        2.40        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46         8.45         9.96        37.51        31.30         0.39 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

  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 
                     129.27                      140.38 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                      16.04                       18.05 
[1] "0.2 - 129.3 (16.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.5"
D29V2, continuous
D29V3, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   117  48
  DEL PEAK  2(1P33) WILD-TYPE 312 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    117   48
  DEL PEAK  2(1P33) WILD-TYPE  312  111
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  COLON                        117                         312
  RECTUM                        48                         111
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  2(1P33) MUTATED        19        0        7        47         1
  DEL PEAK  2(1P33) WILD-TYPE      83        1       29       118         9
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P33) MUTATED           0         7          5         24
  DEL PEAK  2(1P33) WILD-TYPE         3        19         17         52
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  2(1P33) MUTATED           19       27         5         0
  DEL PEAK  2(1P33) WILD-TYPE         33       33        20         1
D29V4, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                           19                          83
  STAGE IA                           0                           1
  STAGE II                           7                          29
  STAGE IIA                         47                         118
  STAGE IIB                          1                           9
  STAGE IIC                          0                           3
  STAGE III                          7                          19
  STAGE IIIA                         5                          17
  STAGE IIIB                        24                          52
  STAGE IIIC                        19                          33
  STAGE IV                          27                          33
  STAGE IVA                          5                          20
  STAGE IVB                          0                           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                          T0+T1  T2  T3  T4
  DEL PEAK  2(1P33) MUTATED       4  23 121  18
  DEL PEAK  2(1P33) WILD-TYPE    16  82 282  44
D29V5, multiclass
       clus
vv      DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T0+T1                         4                          16
  T2                           23                          82
  T3                          121                         282
  T4                           18                          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  2(1P33) MUTATED    79  50  37
  DEL PEAK  2(1P33) WILD-TYPE 256  96  71
D29V6, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        79                         256
  N1                        50                          96
  N2                        37                          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  2(1P33) MUTATED   113  31   1   0  20
  DEL PEAK  2(1P33) WILD-TYPE 330  41   8   1  38
D29V7, multiclass
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  M0                        113                         330
  M1                         31                          41
  M1A                         1                           8
  M1B                         0                           1
  MX                         20                          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"
D29V8, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    76  91
  DEL PEAK  2(1P33) WILD-TYPE 201 224
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     76   91
  DEL PEAK  2(1P33) WILD-TYPE  201  224
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        76                         201
  MALE                          91                         224
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                    108
  DEL PEAK  2(1P33) WILD-TYPE                  265
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                               9
  DEL PEAK  2(1P33) WILD-TYPE                            46
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                      46
  DEL PEAK  2(1P33) WILD-TYPE                    97
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                                1
  DEL PEAK  2(1P33) WILD-TYPE                             12
D29V9, multiclass
                                clus
vv                               DEL PEAK  2(1P33) MUTATED
  COLON ADENOCARCINOMA                                 108
  COLON MUCINOUS ADENOCARCINOMA                          9
  RECTAL ADENOCARCINOMA                                 46
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  2(1P33) WILD-TYPE
  COLON ADENOCARCINOMA                                   265
  COLON MUCINOUS ADENOCARCINOMA                           46
  RECTAL ADENOCARCINOMA                                   97
  RECTAL MUCINOUS ADENOCARCINOMA                          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"
D29V10, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED     3 164
  DEL PEAK  2(1P33) WILD-TYPE   6 419
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED      3  164
  DEL PEAK  2(1P33) WILD-TYPE    6  419
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                          3                           6
  YES                       164                         419
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  2(1P33) MUTATED   109   2  14   7
  DEL PEAK  2(1P33) WILD-TYPE 317   3  22  20
D29V11, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                       109                         317
  R1                         2                           3
  R2                        14                          22
  RX                         7                          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"
D29V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(1P33) MUTATED                                  1     4
  DEL PEAK  2(1P33) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P33) MUTATED                          15    83
  DEL PEAK  2(1P33) WILD-TYPE                        29   209
D29V13, multiclass
                                  clus
vv                                 DEL PEAK  2(1P33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               15
  WHITE                                                   83
                                  clus
vv                                 DEL PEAK  2(1P33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 29
  WHITE                                                    209
[1] 4 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  3(1P13.2) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1P13.2) MUTATED   124  36
  DEL PEAK  3(1P13.2) WILD-TYPE 333  70
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          160                           403 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           36                            70 
$`DEL PEAK  3(1P13.2) 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-3520 
       23.87        52.44         5.03        38.99         9.07        24.03 
TCGA-AA-3522 TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3673 TCGA-AA-3685 
       37.05        21.01        13.94        19.99        50.04        37.05 
TCGA-AA-3688 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3855 
       19.00         0.99        38.99        37.02         0.99        32.05 
TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 
       31.07        17.03        24.03         2.01        12.99         2.01 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00Q 
        2.01        21.99        13.05         7.96        38.04        42.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01X 
       15.02        32.02        31.00         1.02        33.04        26.01 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 
        2.96         2.01        41.00        40.96         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AY-A69D 
        1.02         0.20         0.43         0.92        14.50         5.52 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 
        5.65        32.94         5.13        65.00        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6716 
        5.23         3.19         2.24         3.06         2.14         0.26 
TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-6163 TCGA-CM-6164 
        2.01         8.02        13.02        22.03        14.04        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-6531 
       13.02        15.02        11.08        10.06        13.51        17.75 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 
        1.32        15.12        14.30        13.41        11.38        92.75 
TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 
       49.91       131.51         6.12        14.04        26.47        13.38 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
        1.55        16.24        33.67        35.41         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 
       23.51        61.87        36.72        36.00        91.79        46.75 
TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 
        4.11         5.98        26.99        24.13        17.23        13.55 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 
       14.50        15.39        32.02         1.02        24.00        34.03 
TCGA-AG-3594 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3909 
        2.01        29.98         1.02        19.99         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
       28.04        36.03        25.97        23.01        12.00        70.03 
TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 
        1.94        38.04         0.49         0.69        10.19         9.37 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA 
       11.01        12.99        13.97        36.00        30.05       126.44 
TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6511 
       41.36       129.27         0.49        20.55        17.00        15.85 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       11.51        13.64        11.97        14.86         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 
        0.69         0.76        18.28        47.08 

$`DEL PEAK  3(1P13.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 
       44.91        45.60        13.94        37.05        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-A6-5666 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-A6-6648 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-A5ZU 
       19.66        20.28        16.24        24.92        61.84         9.63 
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-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-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-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-3678 TCGA-AA-3679 
        2.01        14.01         0.92        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       11.01         5.98        36.00         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-3844 TCGA-AA-3846 TCGA-AA-3851 
       17.98        15.95        36.95        14.93        17.03        33.07 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       36.03         0.99        31.07        53.00        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-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-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-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-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-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-6895 TCGA-AD-6963 
        0.07        21.37         4.21        56.55         0.72         0.10 
TCGA-AD-6964 TCGA-AM-5820 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.76         0.46        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
        0.20        21.44        17.82         5.19        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 
       58.39         1.41        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-5796 
       49.41         6.77       100.01        11.74         1.94         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         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        21.01         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 
       37.02         8.02        26.04        27.02        29.06        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-6165 TCGA-CM-6166 TCGA-CM-6167 
       17.03        15.02        12.00        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       12.99        14.04        11.01        12.95        13.05        11.08 
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-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        20.42        18.25         7.92        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-D5-6926 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-A0XF TCGA-DM-A1D0 
       12.00        10.26       119.70        24.43        38.20       130.65 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       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-G4-6304 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-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       26.17        47.15        52.80         5.06         2.79         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       17.29        14.76        17.95        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       37.74        10.39         8.45        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       12.00         8.02         7.07         2.01         1.02        46.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       48.03        32.02        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       20.98        13.94         6.02        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 
       49.97        38.96        61.97        41.00         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        4.60         1.81         6.05         6.05         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
       13.97        60.03         7.99        10.98        15.02        12.00 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02         7.10        12.95        13.05        10.06         5.29 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        18.28        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
        8.61        10.78        17.46         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 
       31.30         0.39         0.53         1.12         0.46        55.76 
TCGA-G5-6641 
       26.43 

  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                       15.685                        18.050 
[1] "0.2 - 131.5 (15.7)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.5"
D30V2, continuous
D30V3, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED   115  50
  DEL PEAK  3(1P13.2) WILD-TYPE 314 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED    115   50
  DEL PEAK  3(1P13.2) WILD-TYPE  314  109
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  COLON                          115                           314
  RECTUM                          50                           109
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  3(1P13.2) MUTATED        19        0        8        46         1
  DEL PEAK  3(1P13.2) WILD-TYPE      83        1       28       119         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1P13.2) MUTATED           2         5          4         23
  DEL PEAK  3(1P13.2) WILD-TYPE         1        21         18         53
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  3(1P13.2) MUTATED           20       28         5         0
  DEL PEAK  3(1P13.2) WILD-TYPE         32       32        20         1
D30V4, multiclass
            clus
vv           DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  STAGE I                             19                            83
  STAGE IA                             0                             1
  STAGE II                             8                            28
  STAGE IIA                           46                           119
  STAGE IIB                            1                             9
  STAGE IIC                            2                             1
  STAGE III                            5                            21
  STAGE IIIA                           4                            18
  STAGE IIIB                          23                            53
  STAGE IIIC                          20                            32
  STAGE IV                            28                            32
  STAGE IVA                            5                            20
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK  3(1P13.2) MUTATED       5  21 121  19
  DEL PEAK  3(1P13.2) WILD-TYPE    15  84 282  43
D30V5, multiclass
       clus
vv      DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  T0+T1                           5                            15
  T2                             21                            84
  T3                            121                           282
  T4                             19                            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  3(1P13.2) MUTATED    79  45  42
  DEL PEAK  3(1P13.2) WILD-TYPE 256 101  66
D30V6, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  N0                          79                           256
  N1                          45                           101
  N2                          42                            66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  3(1P13.2) MUTATED   115  33   0   0  17
  DEL PEAK  3(1P13.2) WILD-TYPE 328  39   9   1  41
D30V7, multiclass
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  M0                          115                           328
  M1                           33                            39
  M1A                           0                             9
  M1B                           0                             1
  MX                           17                            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"
D30V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED    75  92
  DEL PEAK  3(1P13.2) WILD-TYPE 202 223
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     75   92
  DEL PEAK  3(1P13.2) WILD-TYPE  202  223
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  FEMALE                          75                           202
  MALE                            92                           223
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                    106
  DEL PEAK  3(1P13.2) WILD-TYPE                  267
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                               9
  DEL PEAK  3(1P13.2) WILD-TYPE                            46
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                      47
  DEL PEAK  3(1P13.2) WILD-TYPE                    96
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                                2
  DEL PEAK  3(1P13.2) WILD-TYPE                             11
D30V9, multiclass
                                clus
vv                               DEL PEAK  3(1P13.2) MUTATED
  COLON ADENOCARCINOMA                                   106
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   47
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK  3(1P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     267
  COLON MUCINOUS ADENOCARCINOMA                             46
  RECTAL ADENOCARCINOMA                                     96
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D30V10, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED     4 163
  DEL PEAK  3(1P13.2) WILD-TYPE   5 420
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED      4  163
  DEL PEAK  3(1P13.2) WILD-TYPE    5  420
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  NO                            4                             5
  YES                         163                           420
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1P13.2) MUTATED   111   1  14   8
  DEL PEAK  3(1P13.2) WILD-TYPE 315   4  22  19
D30V11, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  R0                         111                           315
  R1                           1                             4
  R2                          14                            22
  RX                           8                            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"
D30V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(1P13.2) MUTATED                                  1     4
  DEL PEAK  3(1P13.2) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1P13.2) MUTATED                          15    85
  DEL PEAK  3(1P13.2) WILD-TYPE                        29   207
D30V13, multiclass
                                  clus
vv                                 DEL PEAK  3(1P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 15
  WHITE                                                     85
                                  clus
vv                                 DEL PEAK  3(1P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   29
  WHITE                                                      207
[1] 4 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  4(2P12) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2P12) MUTATED    16   3
  DEL PEAK  4(2P12) WILD-TYPE 441 103
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         19                         544 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                          3                         103 
$`DEL PEAK  4(2P12) MUTATED`
TCGA-A6-2677 TCGA-AA-3511 TCGA-AA-3560 TCGA-AA-3842 TCGA-AA-3939 TCGA-AA-A01S 
       17.79         6.97        19.99        37.02        12.99         1.02 
TCGA-CM-5341 TCGA-G4-6626 TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 
       29.06        46.75        15.39        32.02         1.02         6.05 
TCGA-AG-3609 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-A00H TCGA-AG-A02X TCGA-DC-6156 
       19.99         1.02        28.04        25.97        41.00        15.02 
TCGA-F5-6571 
       31.30 

$`DEL PEAK  4(2P12) 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-A6-2678 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-A6-5661 
       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-A6-6651 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-3514 TCGA-AA-3516 
        1.02        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-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-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-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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98        15.02        15.02         0.99        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-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-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-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.10         0.76         0.20         0.43         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
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-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        21.01         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-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-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 
       13.02        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-D5-6531 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-D5-6932 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-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-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-F4-6808 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-G4-6627 
       26.04        13.78        35.80        26.17        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       52.80         4.11         5.06         2.79         5.98         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       26.99        17.29        14.76        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50         8.45        20.02        10.39        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       15.02        12.99        12.00        13.97        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        37.51        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                       1.02                        0.07 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                      46.75                      140.38 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                      19.99                       17.90 
[1] "1.0 - 46.8 (20.0)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "1"  
D31V2, continuous
D31V3, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     8  13
  DEL PEAK  4(2P12) WILD-TYPE 421 146
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      8   13
  DEL PEAK  4(2P12) WILD-TYPE  421  146
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  COLON                          8                         421
  RECTUM                        13                         146
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  4(2P12) MUTATED         2        0        1         7         0
  DEL PEAK  4(2P12) WILD-TYPE     100        1       35       158        10
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  4(2P12) MUTATED           0         1          2          1
  DEL PEAK  4(2P12) WILD-TYPE         3        25         20         75
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  4(2P12) MUTATED            5        1         1         0
  DEL PEAK  4(2P12) WILD-TYPE         47       59        24         1
D31V4, multiclass
            clus
vv           DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  STAGE I                            2                         100
  STAGE IA                           0                           1
  STAGE II                           1                          35
  STAGE IIA                          7                         158
  STAGE IIB                          0                          10
  STAGE IIC                          0                           3
  STAGE III                          1                          25
  STAGE IIIA                         2                          20
  STAGE IIIB                         1                          75
  STAGE IIIC                         5                          47
  STAGE IV                           1                          59
  STAGE IVA                          1                          24
  STAGE IVB                          0                           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                          T0+T1  T2  T3  T4
  DEL PEAK  4(2P12) MUTATED       0   4  15   2
  DEL PEAK  4(2P12) WILD-TYPE    20 101 388  60
D31V5, multiclass
       clus
vv      DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  T0+T1                         0                          20
  T2                            4                         101
  T3                           15                         388
  T4                            2                          60
[1] 4 2
[1] TRUE
[1] "dimension 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(2P12) MUTATED    10   5   6
  DEL PEAK  4(2P12) WILD-TYPE 325 141 102
D31V6, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  N0                        10                         325
  N1                         5                         141
  N2                         6                         102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK  4(2P12) MUTATED    18   1   1   0   1
  DEL PEAK  4(2P12) WILD-TYPE 425  71   8   1  57
D31V7, multiclass
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  M0                         18                         425
  M1                          1                          71
  M1A                         1                           8
  M1B                         0                           1
  MX                          1                          57
[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"
D31V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    11  10
  DEL PEAK  4(2P12) WILD-TYPE 266 305
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     11   10
  DEL PEAK  4(2P12) WILD-TYPE  266  305
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  FEMALE                        11                         266
  MALE                          10                         305
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                      8
  DEL PEAK  4(2P12) WILD-TYPE                  365
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                               0
  DEL PEAK  4(2P12) WILD-TYPE                            55
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                      11
  DEL PEAK  4(2P12) WILD-TYPE                   132
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                                1
  DEL PEAK  4(2P12) WILD-TYPE                             12
D31V9, multiclass
                                clus
vv                               DEL PEAK  4(2P12) MUTATED
  COLON ADENOCARCINOMA                                   8
  COLON MUCINOUS ADENOCARCINOMA                          0
  RECTAL ADENOCARCINOMA                                 11
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  4(2P12) WILD-TYPE
  COLON ADENOCARCINOMA                                   365
  COLON MUCINOUS ADENOCARCINOMA                           55
  RECTAL ADENOCARCINOMA                                  132
  RECTAL MUCINOUS ADENOCARCINOMA                          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"
D31V10, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     1  20
  DEL PEAK  4(2P12) WILD-TYPE   8 563
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      1   20
  DEL PEAK  4(2P12) WILD-TYPE    8  563
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  NO                          1                           8
  YES                        20                         563
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(2P12) MUTATED    18   0   1   0
  DEL PEAK  4(2P12) WILD-TYPE 408   5  35  27
D31V11, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  R0                        18                         408
  R1                         0                           5
  R2                         1                          35
  RX                         0                          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"
D31V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2P12) MUTATED                                  0     0
  DEL PEAK  4(2P12) WILD-TYPE                                1    12
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2P12) MUTATED                           0     6
  DEL PEAK  4(2P12) WILD-TYPE                        44   286
D31V13, multiclass
                                  clus
vv                                 DEL PEAK  4(2P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                0
  WHITE                                                    6
                                  clus
vv                                 DEL PEAK  4(2P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                     12
  BLACK OR AFRICAN AMERICAN                                 44
  WHITE                                                    286
[1] 4 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  5(2Q22.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q22.1) MUTATED    24   7
  DEL PEAK  5(2Q22.1) WILD-TYPE 433  99
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           31                           532 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                            7                            99 
$`DEL PEAK  5(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 TCGA-AG-3609 
       44.32       131.51       117.07         1.55        46.75        19.99 
TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A02X TCGA-DC-6682 TCGA-F5-6571 
       36.03        25.97        15.95        41.00        13.05        31.30 
TCGA-F5-6814 
        0.53 

$`DEL PEAK  5(2Q22.1) 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-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 
       17.79        44.91        35.11        45.60        13.94        15.52 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 
       37.05        37.25        16.04        34.65        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-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       24.13         8.38        25.08        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-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        61.84        52.44         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-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         1.02        13.02        38.99         1.02         9.07 
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-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-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        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-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-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-3851 TCGA-AA-3854 
       38.99        36.95        14.93        17.03        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-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-3975 
        2.01        21.99        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-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        17.03         4.01        27.02        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-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-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.19         5.52        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-5255 TCGA-CA-5256 
        5.23        11.74         3.19         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        21.01         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-5344 TCGA-CM-5348 TCGA-CM-5349 
       27.02        13.02        29.06        22.03        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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
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-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        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-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        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-A1HB 
       92.75        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-A28K TCGA-DM-A28M TCGA-F4-6459 
      119.93        35.97        60.79        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-F4-6805 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-G4-6298 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-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        91.79        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       36.00         7.10        30.05        12.95        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         9.96        37.51        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        1.02         0.66         0.69         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                         0.53                          0.07 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                        24.00                         17.77 
[1] "0.5 - 131.5 (24.0)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1"  
D32V2, continuous
D32V3, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    24  10
  DEL PEAK  5(2Q22.1) WILD-TYPE 405 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     24   10
  DEL PEAK  5(2Q22.1) WILD-TYPE  405  149
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  COLON                           24                           405
  RECTUM                          10                           149
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  5(2Q22.1) MUTATED         2        0        1        15         0
  DEL PEAK  5(2Q22.1) WILD-TYPE     100        1       35       150        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  5(2Q22.1) MUTATED           0         2          1          4
  DEL PEAK  5(2Q22.1) WILD-TYPE         3        24         21         72
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  5(2Q22.1) MUTATED            6        2         1         0
  DEL PEAK  5(2Q22.1) WILD-TYPE         46       58        24         1
D32V4, multiclass
            clus
vv           DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  STAGE I                              2                           100
  STAGE IA                             0                             1
  STAGE II                             1                            35
  STAGE IIA                           15                           150
  STAGE IIB                            0                            10
  STAGE IIC                            0                             3
  STAGE III                            2                            24
  STAGE IIIA                           1                            21
  STAGE IIIB                           4                            72
  STAGE IIIC                           6                            46
  STAGE IV                             2                            58
  STAGE IVA                            1                            24
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK  5(2Q22.1) MUTATED       0   4  26   4
  DEL PEAK  5(2Q22.1) WILD-TYPE    20 101 377  58
D32V5, multiclass
       clus
vv      DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T0+T1                           0                            20
  T2                              4                           101
  T3                             26                           377
  T4                              4                            58
[1] 4 2
[1] TRUE
[1] "dimension 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(2Q22.1) MUTATED    18   8   8
  DEL PEAK  5(2Q22.1) WILD-TYPE 317 138 100
D32V6, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          18                           317
  N1                           8                           138
  N2                           8                           100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  5(2Q22.1) MUTATED    29   2   1   0   2
  DEL PEAK  5(2Q22.1) WILD-TYPE 414  70   8   1  56
D32V7, multiclass
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  M0                           29                           414
  M1                            2                            70
  M1A                           1                             8
  M1B                           0                             1
  MX                            2                            56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    14  20
  DEL PEAK  5(2Q22.1) WILD-TYPE 263 295
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     14   20
  DEL PEAK  5(2Q22.1) WILD-TYPE  263  295
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          14                           263
  MALE                            20                           295
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                     21
  DEL PEAK  5(2Q22.1) WILD-TYPE                  352
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                               3
  DEL PEAK  5(2Q22.1) WILD-TYPE                            52
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                       9
  DEL PEAK  5(2Q22.1) WILD-TYPE                   134
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                                0
  DEL PEAK  5(2Q22.1) WILD-TYPE                             13
D32V9, multiclass
                                clus
vv                               DEL PEAK  5(2Q22.1) MUTATED
  COLON ADENOCARCINOMA                                    21
  COLON MUCINOUS ADENOCARCINOMA                            3
  RECTAL ADENOCARCINOMA                                    9
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               DEL PEAK  5(2Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     352
  COLON MUCINOUS ADENOCARCINOMA                             52
  RECTAL ADENOCARCINOMA                                    134
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D32V10, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     0  34
  DEL PEAK  5(2Q22.1) WILD-TYPE   9 549
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      0   34
  DEL PEAK  5(2Q22.1) WILD-TYPE    9  549
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                            0                             9
  YES                          34                           549
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q22.1) MUTATED    25   0   2   1
  DEL PEAK  5(2Q22.1) WILD-TYPE 401   5  34  26
D32V11, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  R0                          25                           401
  R1                           0                             5
  R2                           2                            34
  RX                           1                            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"
D32V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(2Q22.1) MUTATED                                  1     2
  DEL PEAK  5(2Q22.1) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q22.1) MUTATED                           1    12
  DEL PEAK  5(2Q22.1) WILD-TYPE                        43   280
D32V13, multiclass
                                  clus
vv                                 DEL PEAK  5(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     12
                                  clus
vv                                 DEL PEAK  5(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   43
  WHITE                                                      280
[1] 4 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  6(2Q37.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(2Q37.2) MUTATED    22   7
  DEL PEAK  6(2Q37.2) WILD-TYPE 435  99
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                           29                           534 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                            7                            99 
$`DEL PEAK  6(2Q37.2) MUTATED`
TCGA-A6-2684 TCGA-A6-2686 TCGA-AA-3511 TCGA-AA-3522 TCGA-AA-3560 TCGA-AA-3664 
       37.05        16.04         6.97        37.05        19.99        54.02 
TCGA-AA-3666 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-A02F 
        2.01        37.02         0.99        18.05        12.99        39.98 
TCGA-CA-5254 TCGA-CA-5797 TCGA-CK-4951 TCGA-D5-6534 TCGA-DM-A1D4 TCGA-DM-A1D6 
        2.24         3.29        70.16         7.92        92.75        49.91 
TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6805 TCGA-AG-3600 TCGA-AG-3883 TCGA-AG-3896 
       26.47        13.38        16.31         6.05         1.02         1.02 
TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A011 TCGA-DY-A1DE TCGA-F5-6571 
       36.03        25.97        37.02       129.27        31.30 

$`DEL PEAK  6(2Q37.2) 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-A6-2683 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       15.52        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-A6-6648 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-3514 TCGA-AA-3516 TCGA-AA-3517 
       35.01        58.03        63.98         1.02        13.02        38.99 
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-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-3561 TCGA-AA-3562 
       17.95        29.95        23.01        20.98        13.94        19.99 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.05         6.97        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        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-3841 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        36.95        14.93 
TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       17.03        33.07        36.03        32.05         0.99        31.07 
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-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-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-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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98        15.02        15.02         0.99        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-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         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-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-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.10         0.76         0.20         0.43         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       14.50        27.09        16.31         0.95        15.75         0.20 
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-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-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        1.94         3.06         2.14         3.25         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-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.01         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-D5-6535 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-D5-6898 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-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        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-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-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       35.87         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-G4-6306 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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV 
        4.11         5.06         2.79         5.98         5.59        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       17.29        14.76        24.13        17.95        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       13.55        19.10        12.72        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
        8.45        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A014 
        0.99        20.98        13.94         6.02        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         7.10        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       17.46        11.97         8.45         9.96        37.51        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                         0.99                          0.07 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                       129.27                        140.38 
  DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE 
                       19.990                        17.835 
[1] "1.0 - 129.3 (20.0)" "0.1 - 140.4 (17.8)"
[1] "hr=" "1.1"
D33V2, continuous
D33V3, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q37.2) MUTATED    21  10
  DEL PEAK  6(2Q37.2) WILD-TYPE 408 149
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.2) MUTATED     21   10
  DEL PEAK  6(2Q37.2) WILD-TYPE  408  149
        clus
vv       DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  COLON                           21                           408
  RECTUM                          10                           149
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  6(2Q37.2) MUTATED         4        0        2        17         0
  DEL PEAK  6(2Q37.2) WILD-TYPE      98        1       34       148        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(2Q37.2) MUTATED           0         1          1          1
  DEL PEAK  6(2Q37.2) WILD-TYPE         3        25         21         75
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  6(2Q37.2) MUTATED            4        1         0         0
  DEL PEAK  6(2Q37.2) WILD-TYPE         48       59        25         1
D33V4, multiclass
            clus
vv           DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  STAGE I                              4                            98
  STAGE IA                             0                             1
  STAGE II                             2                            34
  STAGE IIA                           17                           148
  STAGE IIB                            0                            10
  STAGE IIC                            0                             3
  STAGE III                            1                            25
  STAGE IIIA                           1                            21
  STAGE IIIB                           1                            75
  STAGE IIIC                           4                            48
  STAGE IV                             1                            59
  STAGE IVA                            0                            25
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK  6(2Q37.2) MUTATED       1   4  25   1
  DEL PEAK  6(2Q37.2) WILD-TYPE    19 101 378  61
D33V5, multiclass
       clus
vv      DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  T0+T1                           1                            19
  T2                              4                           101
  T3                             25                           378
  T4                              1                            61
[1] 4 2
[1] TRUE
[1] "dimension 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(2Q37.2) MUTATED    23   4   4
  DEL PEAK  6(2Q37.2) WILD-TYPE 312 142 104
D33V6, multiclass
    clus
vv   DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  N0                          23                           312
  N1                           4                           142
  N2                           4                           104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  6(2Q37.2) MUTATED    30   1   0   0   0
  DEL PEAK  6(2Q37.2) WILD-TYPE 413  71   9   1  58
D33V7, multiclass
     clus
vv    DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  M0                           30                           413
  M1                            1                            71
  M1A                           0                             9
  M1B                           0                             1
  MX                            0                            58
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q37.2) MUTATED    17  14
  DEL PEAK  6(2Q37.2) WILD-TYPE 260 301
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.2) MUTATED     17   14
  DEL PEAK  6(2Q37.2) WILD-TYPE  260  301
        clus
vv       DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  FEMALE                          17                           260
  MALE                            14                           301
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  6(2Q37.2) MUTATED                     18
  DEL PEAK  6(2Q37.2) WILD-TYPE                  355
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  6(2Q37.2) MUTATED                               3
  DEL PEAK  6(2Q37.2) WILD-TYPE                            52
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  6(2Q37.2) MUTATED                       9
  DEL PEAK  6(2Q37.2) WILD-TYPE                   134
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  6(2Q37.2) MUTATED                                0
  DEL PEAK  6(2Q37.2) WILD-TYPE                             13
D33V9, multiclass
                                clus
vv                               DEL PEAK  6(2Q37.2) MUTATED
  COLON ADENOCARCINOMA                                    18
  COLON MUCINOUS ADENOCARCINOMA                            3
  RECTAL ADENOCARCINOMA                                    9
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               DEL PEAK  6(2Q37.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     355
  COLON MUCINOUS ADENOCARCINOMA                             52
  RECTAL ADENOCARCINOMA                                    134
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D33V10, binary
                               cls
clus                              0   1
  DEL PEAK  6(2Q37.2) MUTATED     0  31
  DEL PEAK  6(2Q37.2) WILD-TYPE   9 552
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.2) MUTATED      0   31
  DEL PEAK  6(2Q37.2) WILD-TYPE    9  552
     clus
vv    DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  NO                            0                             9
  YES                          31                           552
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(2Q37.2) MUTATED    23   1   1   1
  DEL PEAK  6(2Q37.2) WILD-TYPE 403   4  35  26
D33V11, multiclass
    clus
vv   DEL PEAK  6(2Q37.2) MUTATED DEL PEAK  6(2Q37.2) WILD-TYPE
  R0                          23                           403
  R1                           1                             4
  R2                           1                            35
  RX                           1                            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"
D33V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(2Q37.2) MUTATED                                  0     2
  DEL PEAK  6(2Q37.2) WILD-TYPE                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(2Q37.2) MUTATED                           0    11
  DEL PEAK  6(2Q37.2) WILD-TYPE                        44   281
D33V13, multiclass
                                  clus
vv                                 DEL PEAK  6(2Q37.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     11
                                  clus
vv                                 DEL PEAK  6(2Q37.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   44
  WHITE                                                      281
[1] 4 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  7(3P26.3) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P26.3) MUTATED    68  17
  DEL PEAK  7(3P26.3) WILD-TYPE 389  89
  DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE 
                           85                           478 
  DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE 
                           17                            89 
$`DEL PEAK  7(3P26.3) 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-3662 TCGA-AA-3679 
        6.97        38.99         9.07        29.00         6.05        15.02 
TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3870 
       85.05         0.99        32.05        31.07        17.03        29.98 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 
        2.01        12.99         2.01         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-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3727 
       13.55        12.72        14.50         2.01        24.00         0.99 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-A02N TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 
        1.02        19.99        61.97         0.49        10.19         6.05 
TCGA-CI-6624 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6810 
        4.73        13.05         5.29        17.69        16.31         0.39 
TCGA-G5-6233 
       18.28 

$`DEL PEAK  7(3P26.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 
        5.06        37.02        46.65        43.76        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 
       42.28        44.91        35.11        45.60        13.94        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       37.25        16.04        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-A6-6780 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-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        61.84        52.44         1.02         3.02         1.02 
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-3518 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       13.02         1.02        24.03        37.05        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-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-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-3955 TCGA-AA-3956 TCGA-AA-3971 
       33.01        26.01        24.00        20.98        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
       13.05        34.06        26.01        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J 
       27.02        38.04        19.00        30.02        34.03        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-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        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-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
        2.96        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-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-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.76         0.20         0.46         0.92        14.50        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-AY-A69D TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        5.52        75.25        50.37        58.39         1.41        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-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        6.77       100.01        29.56         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-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        21.01         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-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-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-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-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       14.99        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       18.25         4.50        17.13        12.49        16.14        15.58 
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-D5-6927 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-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-F4-6461 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-F4-6806 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-G4-6298 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-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 
        5.06         2.79         5.59        17.29        14.76        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.95        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
        8.45        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 
       32.02         8.02         7.07         1.02         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3732 
       15.95        19.99        19.99         7.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.96        41.00        38.04         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        4.60         1.81         6.05         6.97         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       12.95        10.06       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE 
                       13.380                        19.085 
[1] "0.2 - 85.0 (13.4)"  "0.1 - 140.4 (19.1)"
[1] "hr=" "1.7"
D34V2, continuous
D34V3, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.3) MUTATED    67  20
  DEL PEAK  7(3P26.3) WILD-TYPE 362 139
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.3) MUTATED     67   20
  DEL PEAK  7(3P26.3) WILD-TYPE  362  139
        clus
vv       DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE
  COLON                           67                           362
  RECTUM                          20                           139
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  7(3P26.3) MUTATED         8        0        3        24         0
  DEL PEAK  7(3P26.3) WILD-TYPE      94        1       33       141        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P26.3) MUTATED           1         5          2         13
  DEL PEAK  7(3P26.3) WILD-TYPE         2        21         20         63
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  7(3P26.3) MUTATED            8       19         5         0
  DEL PEAK  7(3P26.3) WILD-TYPE         44       41        20         1
D34V4, multiclass
            clus
vv           DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE
  STAGE I                              8                            94
  STAGE IA                             0                             1
  STAGE II                             3                            33
  STAGE IIA                           24                           141
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           2                            20
  STAGE IIIB                          13                            63
  STAGE IIIC                           8                            44
  STAGE IV                            19                            41
  STAGE IVA                            5                            20
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK  7(3P26.3) MUTATED       2   8  68  11
  DEL PEAK  7(3P26.3) WILD-TYPE    18  97 335  51
D34V5, multiclass
       clus
vv      DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE
  T0+T1                           2                            18
  T2                              8                            97
  T3                             68                           335
  T4                             11                            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  7(3P26.3) MUTATED    38  28  23
  DEL PEAK  7(3P26.3) WILD-TYPE 297 118  85
D34V6, multiclass
    clus
vv   DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE
  N0                          38                           297
  N1                          28                           118
  N2                          23                            85
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  7(3P26.3) MUTATED    55  21   3   0   8
  DEL PEAK  7(3P26.3) WILD-TYPE 388  51   6   1  50
D34V7, multiclass
     clus
vv    DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE
  M0                           55                           388
  M1                           21                            51
  M1A                           3                             6
  M1B                           0                             1
  MX                            8                            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"
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.3) MUTATED    40  49
  DEL PEAK  7(3P26.3) WILD-TYPE 237 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.3) MUTATED     40   49
  DEL PEAK  7(3P26.3) WILD-TYPE  237  266
        clus
vv       DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE
  FEMALE                          40                           237
  MALE                            49                           266
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  7(3P26.3) MUTATED                     63
  DEL PEAK  7(3P26.3) WILD-TYPE                  310
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  7(3P26.3) MUTATED                               4
  DEL PEAK  7(3P26.3) WILD-TYPE                            51
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  7(3P26.3) MUTATED                      16
  DEL PEAK  7(3P26.3) WILD-TYPE                   127
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  7(3P26.3) MUTATED                                3
  DEL PEAK  7(3P26.3) WILD-TYPE                             10
D34V9, multiclass
                                clus
vv                               DEL PEAK  7(3P26.3) MUTATED
  COLON ADENOCARCINOMA                                    63
  COLON MUCINOUS ADENOCARCINOMA                            4
  RECTAL ADENOCARCINOMA                                   16
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK  7(3P26.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     310
  COLON MUCINOUS ADENOCARCINOMA                             51
  RECTAL ADENOCARCINOMA                                    127
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P26.3) MUTATED     2  87
  DEL PEAK  7(3P26.3) WILD-TYPE   7 496
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P26.3) MUTATED      2   87
  DEL PEAK  7(3P26.3) WILD-TYPE    7  496
     clus
vv    DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE
  NO                            2                             7
  YES                          87                           496
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(3P26.3) MUTATED    60   0  11   5
  DEL PEAK  7(3P26.3) WILD-TYPE 366   5  25  22
D34V11, multiclass
    clus
vv   DEL PEAK  7(3P26.3) MUTATED DEL PEAK  7(3P26.3) WILD-TYPE
  R0                          60                           366
  R1                           0                             5
  R2                          11                            25
  RX                           5                            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"
D34V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(3P26.3) MUTATED                                  0     3
  DEL PEAK  7(3P26.3) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P26.3) MUTATED                           6    44
  DEL PEAK  7(3P26.3) WILD-TYPE                        38   248
D34V13, multiclass
                                  clus
vv                                 DEL PEAK  7(3P26.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  6
  WHITE                                                     44
                                  clus
vv                                 DEL PEAK  7(3P26.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   38
  WHITE                                                      248
[1] 4 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  8(3P14.2) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3P14.2) MUTATED    83  21
  DEL PEAK  8(3P14.2) WILD-TYPE 374  85
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                          104                           459 
  DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE 
                           21                            85 
$`DEL PEAK  8(3P14.2) MUTATED`
TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       15.52        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6780 TCGA-A6-A56B 
       29.16        22.52        25.08        21.76        20.12        52.44 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3662 
        9.63         5.03        38.99         1.02         9.07         6.05 
TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3811 
       54.02         0.92        11.01        37.05        85.05         0.99 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3966 
       32.05        31.07        17.03         2.01        12.99         2.01 
TCGA-AA-3968 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00J 
       21.99        24.00        27.02         7.96        13.94        18.05 
TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02W 
       17.03        27.02         0.99        32.02        31.00        41.00 
TCGA-AD-6548 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       21.37         0.79         1.58         0.43         0.46        14.50 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-6600 TCGA-CA-5797 
       16.31         0.20        75.25         5.65        12.10         3.29 
TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6171 
        0.26         2.01         8.02         5.03        14.04        14.04 
TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       13.05        11.08        11.01        20.19        17.75         1.32 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1DA 
        7.92        17.85        13.41        11.38       119.70         7.50 
TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-G4-6317 TCGA-NH-A6GA TCGA-QG-A5YV 
       35.97       117.07        13.38        36.00         5.98        26.99 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3580 TCGA-AG-3581 
       43.04        19.10        12.72        14.50         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-4007 
        2.01        24.00         1.02        32.98        19.99         1.02 
TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A02G TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 
       17.03         6.02        38.96         0.49        10.19         6.05 
TCGA-CI-6623 TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6508 
        9.37        15.02         7.10        13.05         5.29        20.91 
TCGA-F5-6810 TCGA-G5-6233 
        0.39        18.28 

$`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-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
        5.19         5.52        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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       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-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 
       21.01         2.93       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
        8.02        26.04        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01        15.02        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        29.03        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6674 
       14.99        12.99        13.02        15.02        11.01        12.95 
TCGA-CM-6676 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-D5-6535 TCGA-D5-6537 
       13.51        11.51        20.42        18.25        15.12         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-A0XF TCGA-DM-A1D0 
        1.51        12.00        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       92.75        49.91        13.32        12.59       140.38        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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        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-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       36.72        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-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 
        5.06         2.79         5.59        17.29        14.76        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       17.95        17.23        13.55        37.74        10.39         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        7.99         0.99        29.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.98        13.94        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.04         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
        4.60         1.81         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       60.03         7.99        10.98        11.01        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        15.02        36.00        30.05        12.95        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        19.96        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        8.45         9.96        37.51        31.30        14.86         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  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 
                        14.04                         19.07 
[1] "0.2 - 119.7 (14.0)" "0.1 - 140.4 (19.1)"
[1] "hr=" "1.5"
D35V2, continuous
D35V3, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    81  27
  DEL PEAK  8(3P14.2) WILD-TYPE 348 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     81   27
  DEL PEAK  8(3P14.2) WILD-TYPE  348  132
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  COLON                           81                           348
  RECTUM                          27                           132
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  8(3P14.2) MUTATED        19        0        3        28         0
  DEL PEAK  8(3P14.2) WILD-TYPE      83        1       33       137        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3P14.2) MUTATED           1         5          1         17
  DEL PEAK  8(3P14.2) WILD-TYPE         2        21         21         59
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  8(3P14.2) MUTATED           11       16         6         1
  DEL PEAK  8(3P14.2) WILD-TYPE         41       44        19         0
D35V4, multiclass
            clus
vv           DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  STAGE I                             19                            83
  STAGE IA                             0                             1
  STAGE II                             3                            33
  STAGE IIA                           28                           137
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           1                            21
  STAGE IIIB                          17                            59
  STAGE IIIC                          11                            41
  STAGE IV                            16                            44
  STAGE IVA                            6                            19
  STAGE IVB                            1                             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                            T0+T1  T2  T3  T4
  DEL PEAK  8(3P14.2) MUTATED       7  15  73  15
  DEL PEAK  8(3P14.2) WILD-TYPE    13  90 330  47
D35V5, multiclass
       clus
vv      DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  T0+T1                           7                            13
  T2                             15                            90
  T3                             73                           330
  T4                             15                            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  8(3P14.2) MUTATED    54  31  25
  DEL PEAK  8(3P14.2) WILD-TYPE 281 115  83
D35V6, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  N0                          54                           281
  N1                          31                           115
  N2                          25                            83
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK  8(3P14.2) MUTATED    74  19   3   1  11
  DEL PEAK  8(3P14.2) WILD-TYPE 369  53   6   0  47
D35V7, multiclass
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  M0                           74                           369
  M1                           19                            53
  M1A                           3                             6
  M1B                           1                             0
  MX                           11                            47
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED    48  62
  DEL PEAK  8(3P14.2) WILD-TYPE 229 253
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED     48   62
  DEL PEAK  8(3P14.2) WILD-TYPE  229  253
        clus
vv       DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  FEMALE                          48                           229
  MALE                            62                           253
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  8(3P14.2) MUTATED                     74
  DEL PEAK  8(3P14.2) WILD-TYPE                  299
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(3P14.2) MUTATED                               7
  DEL PEAK  8(3P14.2) WILD-TYPE                            48
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  8(3P14.2) MUTATED                      23
  DEL PEAK  8(3P14.2) WILD-TYPE                   120
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(3P14.2) MUTATED                                3
  DEL PEAK  8(3P14.2) WILD-TYPE                             10
D35V9, multiclass
                                clus
vv                               DEL PEAK  8(3P14.2) MUTATED
  COLON ADENOCARCINOMA                                    74
  COLON MUCINOUS ADENOCARCINOMA                            7
  RECTAL ADENOCARCINOMA                                   23
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK  8(3P14.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     299
  COLON MUCINOUS ADENOCARCINOMA                             48
  RECTAL ADENOCARCINOMA                                    120
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, binary
                               cls
clus                              0   1
  DEL PEAK  8(3P14.2) MUTATED     2 108
  DEL PEAK  8(3P14.2) WILD-TYPE   7 475
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3P14.2) MUTATED      2  108
  DEL PEAK  8(3P14.2) WILD-TYPE    7  475
     clus
vv    DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  NO                            2                             7
  YES                         108                           475
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  8(3P14.2) MUTATED    75   1  11   4
  DEL PEAK  8(3P14.2) WILD-TYPE 351   4  25  23
D35V11, multiclass
    clus
vv   DEL PEAK  8(3P14.2) MUTATED DEL PEAK  8(3P14.2) WILD-TYPE
  R0                          75                           351
  R1                           1                             4
  R2                          11                            25
  RX                           4                            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"
D35V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(3P14.2) MUTATED                                  0     3
  DEL PEAK  8(3P14.2) WILD-TYPE                                1     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3P14.2) MUTATED                           8    53
  DEL PEAK  8(3P14.2) WILD-TYPE                        36   239
D35V13, multiclass
                                  clus
vv                                 DEL PEAK  8(3P14.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     53
                                  clus
vv                                 DEL PEAK  8(3P14.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   36
  WHITE                                                      239
[1] 4 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  9(3Q26.31) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  9(3Q26.31) MUTATED    49  11
  DEL PEAK  9(3Q26.31) WILD-TYPE 408  95
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            60                            503 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                            11                             95 
$`DEL PEAK  9(3Q26.31) MUTATED`
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5666 TCGA-A6-A56B TCGA-AA-3517 
       34.65        14.53        32.45        32.71        52.44        38.99 
TCGA-AA-3519 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3811 TCGA-AA-3855 
        9.07        19.99         6.05        85.05         0.99        32.05 
TCGA-AA-3939 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A01F 
       12.99         2.01        21.99         7.96        13.94        32.02 
TCGA-AA-A01T TCGA-AA-A02R TCGA-AD-A5EK TCGA-AZ-4315 TCGA-AZ-6600 TCGA-CA-5254 
       33.04        22.03         0.43        58.39        12.10         2.24 
TCGA-CA-6716 TCGA-CA-6718 TCGA-CM-4752 TCGA-CM-5862 TCGA-CM-6677 TCGA-CM-6678 
        0.26         0.10        13.02         5.03        11.08        11.01 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 
       13.51        20.19         1.32         7.92        17.85        13.41 
TCGA-D5-6932 TCGA-DM-A1HA TCGA-DM-A282 TCGA-F4-6460 TCGA-G4-6297 TCGA-G4-6317 
       11.38       131.51       139.17        13.38        82.39        36.00 
TCGA-NH-A50T TCGA-QG-A5YV TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3583 
        4.11        26.99        12.72        14.50        32.02         2.01 
TCGA-AG-3728 TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A026 TCGA-AG-A02G 
       29.98        14.01        36.03         1.02         1.94        38.96 
TCGA-CI-6619 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-7002 TCGA-G5-6233 
        6.05        13.05         5.29        19.96        11.97        18.28 

$`DEL PEAK  9(3Q26.31) 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-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5656 
       15.52        37.05        37.25        16.04        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-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       22.06        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       25.08        25.18        24.16        20.61        21.76        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-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-3518 TCGA-AA-3520 TCGA-AA-3522 
        6.97         1.02        13.02         1.02        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-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        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-3663 
       20.98        19.99        13.94        61.02        78.08         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-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-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-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 
       36.03         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-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-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-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-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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98        15.02        15.02         0.99        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-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-A02W TCGA-AA-A02Y 
       39.98         2.01         5.03         0.92        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-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-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
        5.52        75.25        50.37         1.41         5.65        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-6601 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       49.41         6.77       100.01        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-6715 TCGA-CA-6717 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
        0.07         0.33         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        21.01 
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-5341 TCGA-CM-5344 
        8.02        26.04         8.02        27.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        16.01        15.02        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-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 
       14.99        12.26        19.59        11.51        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        15.12         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-D5-6930 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-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-A1DB TCGA-DM-A1HB 
       13.32        12.59       140.38         7.50        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
        7.76         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-F4-6461 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-F4-6806 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-G4-6298 
       35.41        19.43       107.67        28.21         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-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 
       51.75        45.11        39.42        35.93        36.72        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       46.75        47.15        52.80         5.06         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        5.59        17.29        14.76        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       43.04        13.55        19.10        37.74        10.39         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       15.39        20.02        10.39        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07         1.02        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       19.99        19.99         7.99         0.99         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98        51.98        49.97        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       12.95        10.06       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        55.76        47.08        26.43 

  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                        139.17                         140.38 
  DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE 
                        13.725                         18.050 
[1] "0.1 - 139.2 (13.7)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1"  
D36V2, continuous
D36V3, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED    44  15
  DEL PEAK  9(3Q26.31) WILD-TYPE 385 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED     44   15
  DEL PEAK  9(3Q26.31) WILD-TYPE  385  144
        clus
vv       DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  COLON                            44                            385
  RECTUM                           15                            144
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  9(3Q26.31) MUTATED         3        0        2        25         0
  DEL PEAK  9(3Q26.31) WILD-TYPE      99        1       34       140        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(3Q26.31) MUTATED           2         4          0          6
  DEL PEAK  9(3Q26.31) WILD-TYPE         1        22         22         70
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  9(3Q26.31) MUTATED            5       10         3         0
  DEL PEAK  9(3Q26.31) WILD-TYPE         47       50        22         1
D36V4, multiclass
            clus
vv           DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  STAGE I                               3                             99
  STAGE IA                              0                              1
  STAGE II                              2                             34
  STAGE IIA                            25                            140
  STAGE IIB                             0                             10
  STAGE IIC                             2                              1
  STAGE III                             4                             22
  STAGE IIIA                            0                             22
  STAGE IIIB                            6                             70
  STAGE IIIC                            5                             47
  STAGE IV                             10                             50
  STAGE IVA                             3                             22
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK  9(3Q26.31) MUTATED       0   4  47   9
  DEL PEAK  9(3Q26.31) WILD-TYPE    20 101 356  53
D36V5, multiclass
       clus
vv      DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  T0+T1                            0                             20
  T2                               4                            101
  T3                              47                            356
  T4                               9                             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"
                                vv
clus                              N0  N1  N2
  DEL PEAK  9(3Q26.31) MUTATED    33  14  13
  DEL PEAK  9(3Q26.31) WILD-TYPE 302 132  95
D36V6, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  N0                           33                            302
  N1                           14                            132
  N2                           13                             95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK  9(3Q26.31) MUTATED    43  10   2   0   5
  DEL PEAK  9(3Q26.31) WILD-TYPE 400  62   7   1  53
D36V7, multiclass
     clus
vv    DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  M0                            43                            400
  M1                            10                             62
  M1A                            2                              7
  M1B                            0                              1
  MX                             5                             53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V8, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED    22  38
  DEL PEAK  9(3Q26.31) WILD-TYPE 255 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED     22   38
  DEL PEAK  9(3Q26.31) WILD-TYPE  255  277
        clus
vv       DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  FEMALE                           22                            255
  MALE                             38                            277
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK  9(3Q26.31) MUTATED                     42
  DEL PEAK  9(3Q26.31) WILD-TYPE                  331
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(3Q26.31) MUTATED                               2
  DEL PEAK  9(3Q26.31) WILD-TYPE                            53
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK  9(3Q26.31) MUTATED                      11
  DEL PEAK  9(3Q26.31) WILD-TYPE                   132
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(3Q26.31) MUTATED                                4
  DEL PEAK  9(3Q26.31) WILD-TYPE                              9
D36V9, multiclass
                                clus
vv                               DEL PEAK  9(3Q26.31) MUTATED
  COLON ADENOCARCINOMA                                     42
  COLON MUCINOUS ADENOCARCINOMA                             2
  RECTAL ADENOCARCINOMA                                    11
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               DEL PEAK  9(3Q26.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      331
  COLON MUCINOUS ADENOCARCINOMA                              53
  RECTAL ADENOCARCINOMA                                     132
  RECTAL MUCINOUS ADENOCARCINOMA                              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"
D36V10, binary
                                cls
clus                               0   1
  DEL PEAK  9(3Q26.31) MUTATED     1  59
  DEL PEAK  9(3Q26.31) WILD-TYPE   8 524
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  9(3Q26.31) MUTATED      1   59
  DEL PEAK  9(3Q26.31) WILD-TYPE    8  524
     clus
vv    DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  NO                             1                              8
  YES                           59                            524
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  9(3Q26.31) MUTATED    43   1   5   4
  DEL PEAK  9(3Q26.31) WILD-TYPE 383   4  31  23
D36V11, multiclass
    clus
vv   DEL PEAK  9(3Q26.31) MUTATED DEL PEAK  9(3Q26.31) WILD-TYPE
  R0                           43                            383
  R1                            1                              4
  R2                            5                             31
  RX                            4                             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"
D36V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(3Q26.31) MUTATED                                  0     4
  DEL PEAK  9(3Q26.31) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(3Q26.31) MUTATED                           6    27
  DEL PEAK  9(3Q26.31) WILD-TYPE                        38   265
D36V13, multiclass
                                  clus
vv                                 DEL PEAK  9(3Q26.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   6
  WHITE                                                      27
                                  clus
vv                                 DEL PEAK  9(3Q26.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    38
  WHITE                                                       265
[1] 4 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 10(4P16.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4P16.1) MUTATED   142  37
  DEL PEAK 10(4P16.1) WILD-TYPE 315  69
  DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE 
                          179                           384 
  DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE 
                           37                            69 
$`DEL PEAK 10(4P16.1) 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-4616 TCGA-AZ-4684 
        0.95        15.75         0.20         5.52         5.13        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5797 TCGA-CK-5912 
       12.10        29.56         3.19         2.14         3.29        48.20 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5864 TCGA-CM-5868 
        8.02        29.06        22.03        22.98        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 
       14.04        29.03        13.02        15.02        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6923 
       10.06        14.99        13.51        20.19        17.75        12.43 
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-QG-A5YV TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       46.75         4.11        26.99        24.13        17.23        43.04 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3582 
       12.72        37.74        14.50        15.39        10.39         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       46.03        34.03         6.05        29.98         1.02        32.98 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
        1.02        17.03        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H 
       19.99        28.04        36.03        14.04        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6643 
       23.01        12.00        70.03        38.96        41.00         0.69 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6156 
       10.19         6.05         6.05         4.73        12.99        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 
       36.00         7.10        30.05       126.44       129.27        32.61 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 
        2.40        15.85        16.34        16.41        11.97         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-G5-6641 
       31.30        14.86         0.39         0.69        26.43 

$`DEL PEAK 10(4P16.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 
       45.60        37.25        34.65        36.53        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-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6649 
       27.09        22.52        24.13         8.38        25.08        24.16 
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-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-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 
        9.07        24.03        36.03         8.05        19.07        19.07 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01         0.99        14.01        33.99 
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-3667 TCGA-AA-3672 
       13.94        61.02        78.08         6.97        14.01         0.92 
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-3812 
        5.03        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-3844 
        0.99        25.02         1.02        17.98        15.95        14.93 
TCGA-AA-3854 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       36.03        27.02        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        24.00        34.03        16.08        13.05        34.06 
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-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-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-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-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       39.06        51.98         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-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72         0.10         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09        16.31        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-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-6608 TCGA-CA-5254 TCGA-CA-5255 
      100.01         5.23        11.74         1.94         2.24         3.06 
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-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        21.01         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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 
       30.08        16.01        15.02         5.03        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       12.00        16.04        21.99        14.99        12.99        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 TCGA-D5-5538 
       11.01        12.95        13.05        11.08        12.03        12.26 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       19.59        11.51        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-D5-6927 TCGA-D5-6928 
       15.58         7.53        12.39        10.13         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-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32       140.38        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65         7.76       139.17        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-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       16.31        29.59         1.28         0.53        19.43       107.67 
TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       28.21        82.39        74.56        43.07        61.87        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 
       44.68        55.04        51.75        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-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       47.15        52.80         5.06         2.79         5.98         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 
       17.29        14.76        17.95        13.55        19.10        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
        8.45        20.02        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
        7.07         2.01        24.00         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99         0.99        19.99        36.95        13.02 
TCGA-AG-3894 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.01         1.02        17.03         0.99        20.98         6.02 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
       64.01        10.98        51.98        49.97         1.94        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04         0.49         1.45         0.72         4.60         1.81 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 
       11.01        15.02        12.00        13.97        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06         5.29        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       17.46         9.96        37.51         1.02         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 

  DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE 
                       129.27                        140.38 
  DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE 
                       17.030                        18.015 
[1] "0.2 - 129.3 (17.0)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.3"
D37V2, continuous
D37V3, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.1) MUTATED   127  61
  DEL PEAK 10(4P16.1) WILD-TYPE 302  98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.1) MUTATED    127   61
  DEL PEAK 10(4P16.1) WILD-TYPE  302   98
        clus
vv       DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE
  COLON                          127                           302
  RECTUM                          61                            98
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 10(4P16.1) MUTATED        28        0        7        46         2
  DEL PEAK 10(4P16.1) WILD-TYPE      74        1       29       119         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(4P16.1) MUTATED           0         6         10         23
  DEL PEAK 10(4P16.1) WILD-TYPE         3        20         12         53
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 10(4P16.1) MUTATED           22       32        10         0
  DEL PEAK 10(4P16.1) WILD-TYPE         30       28        15         1
D37V4, multiclass
            clus
vv           DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE
  STAGE I                             28                            74
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           46                           119
  STAGE IIB                            2                             8
  STAGE IIC                            0                             3
  STAGE III                            6                            20
  STAGE IIIA                          10                            12
  STAGE IIIB                          23                            53
  STAGE IIIC                          22                            30
  STAGE IV                            32                            28
  STAGE IVA                           10                            15
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 10(4P16.1) MUTATED       6  33 130  21
  DEL PEAK 10(4P16.1) WILD-TYPE    14  72 273  41
D37V5, multiclass
       clus
vv      DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE
  T0+T1                           6                            14
  T2                             33                            72
  T3                            130                           273
  T4                             21                            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 10(4P16.1) MUTATED    88  55  47
  DEL PEAK 10(4P16.1) WILD-TYPE 247  91  61
D37V6, multiclass
    clus
vv   DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE
  N0                          88                           247
  N1                          55                            91
  N2                          47                            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 10(4P16.1) MUTATED   127  35   4   0  19
  DEL PEAK 10(4P16.1) WILD-TYPE 316  37   5   1  39
D37V7, multiclass
     clus
vv    DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE
  M0                          127                           316
  M1                           35                            37
  M1A                           4                             5
  M1B                           0                             1
  MX                           19                            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"
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.1) MUTATED    80 110
  DEL PEAK 10(4P16.1) WILD-TYPE 197 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.1) MUTATED     80  110
  DEL PEAK 10(4P16.1) WILD-TYPE  197  205
        clus
vv       DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE
  FEMALE                          80                           197
  MALE                           110                           205
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 10(4P16.1) MUTATED                    118
  DEL PEAK 10(4P16.1) WILD-TYPE                  255
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(4P16.1) MUTATED                               9
  DEL PEAK 10(4P16.1) WILD-TYPE                            46
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 10(4P16.1) MUTATED                      56
  DEL PEAK 10(4P16.1) WILD-TYPE                    87
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(4P16.1) MUTATED                                4
  DEL PEAK 10(4P16.1) WILD-TYPE                              9
D37V9, multiclass
                                clus
vv                               DEL PEAK 10(4P16.1) MUTATED
  COLON ADENOCARCINOMA                                   118
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   56
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK 10(4P16.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     255
  COLON MUCINOUS ADENOCARCINOMA                             46
  RECTAL ADENOCARCINOMA                                     87
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D37V10, binary
                               cls
clus                              0   1
  DEL PEAK 10(4P16.1) MUTATED     9 181
  DEL PEAK 10(4P16.1) WILD-TYPE   0 402
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4P16.1) MUTATED      9  181
  DEL PEAK 10(4P16.1) WILD-TYPE    0  402
     clus
vv    DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE
  NO                            9                             0
  YES                         181                           402
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4P16.1) MUTATED   138   0  16   5
  DEL PEAK 10(4P16.1) WILD-TYPE 288   5  20  22
D37V11, multiclass
    clus
vv   DEL PEAK 10(4P16.1) MUTATED DEL PEAK 10(4P16.1) WILD-TYPE
  R0                         138                           288
  R1                           0                             5
  R2                          16                            20
  RX                           5                            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"
D37V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(4P16.1) MUTATED                                  1     2
  DEL PEAK 10(4P16.1) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(4P16.1) MUTATED                          13    91
  DEL PEAK 10(4P16.1) WILD-TYPE                        31   201
D37V13, multiclass
                                  clus
vv                                 DEL PEAK 10(4P16.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 13
  WHITE                                                     91
                                  clus
vv                                 DEL PEAK 10(4P16.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   31
  WHITE                                                      201
[1] 4 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 11(4Q22.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q22.1) MUTATED   159  39
  DEL PEAK 11(4Q22.1) WILD-TYPE 298  67
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                          198                           365 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                           39                            67 
$`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-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 
        0.95         0.20         5.52         5.13        83.80        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 
       12.10        29.56         2.14         3.29         1.35       102.44 
TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
       48.20         8.02        13.02        29.06        22.03         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
       15.02        17.03        14.04        29.03        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 
       11.01        13.05        11.08        11.01        14.99        13.51 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6924 
       20.19        17.75         1.32         7.92        15.12        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A1D8 
        9.04        13.41        12.00        11.38        24.43        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28F TCGA-F4-6460 
        7.50        44.32         6.12        14.04        35.97        13.38 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
       16.24        33.67        35.41        28.21         8.35        82.39 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T 
       23.51        45.11        36.72        91.79        46.75         4.11 
TCGA-NH-A6GA TCGA-QG-A5YV TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
        5.98        26.99        24.13        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 
       19.10        12.72        37.74        14.50        15.39         1.02 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3883 
       34.03         6.05        19.99        29.98        32.98         1.02 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03        13.94         6.02        25.97        23.01 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 
       12.00        70.03        64.01         1.94        41.00         0.49 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 
        0.69        10.19         6.05         6.05         4.73        11.01 
TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       12.99        15.02        36.00         7.10        30.05        13.05 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 
      126.44       129.27         2.40        20.91        17.00        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 
       16.34        16.41        11.97         8.45        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        0.39         1.02         0.66         0.69        18.28        26.43 

$`DEL PEAK 11(4Q22.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        46.65        23.38        17.79        42.28 
TCGA-A6-2681 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       45.60        37.25        16.04        14.53        32.91        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-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       22.52        24.13         8.38        25.08        25.18        20.61 
TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.69        24.39        20.12        19.66        16.24        24.92 
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-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 
        1.02        13.02         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        8.05        19.07        19.07        29.00        26.01        12.99 
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-3560 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       20.98        19.99        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       11.01         5.98        19.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       19.04        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 
       15.95        14.93        36.03        32.05        31.07        53.00 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 
       24.03        27.02        29.98        18.05        31.00        12.99 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3971 TCGA-AA-3973 
       24.00        33.01        26.01        24.00        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        19.07         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-A00O TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
        4.01        27.02         0.99        14.99        21.99        34.98 
TCGA-AA-A017 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-A01Z 
        1.02        35.01         1.02        33.04        35.01        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-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-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.46         0.92        27.09        15.75        21.44        17.82 
TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.19        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94        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-5254 
      100.01         5.23        11.74         3.19         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-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-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.01         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-5349 
       37.02         8.02        26.04        27.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       16.01        15.02        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 
       21.99        14.99        12.99        14.04        12.95        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 
       10.06        12.03        12.26        19.59        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25        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-D5-6927 
       15.58         7.53        12.39        10.13        12.43         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
       11.64         1.51        10.26       119.70        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB 
       92.75        49.91        13.32       140.38       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
        7.76       139.17        26.47        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-F4-6704 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-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 
        1.28         0.53        19.43       107.67        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         5.06         2.79 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 
        5.59        17.29        14.76        17.95        10.39         8.45 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
        7.07         2.01        24.00         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        0.99         1.02         0.99         0.99        19.99        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4022 
       17.03        13.02        35.01        14.01        32.02         0.99 
TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       31.00        10.98        51.98        49.97        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 
       38.04         1.45         0.72         4.60         1.81         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        9.37        13.97        60.03         7.99        10.98        15.02 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       12.00        13.97        12.95        10.06         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       57.24        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       19.96        18.28        17.69        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6814 
       10.78        13.64        17.46         9.96        37.51         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        55.76        47.08 

  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 
                       129.27                        140.38 
  DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE 
                        17.03                         18.05 
[1] "0.2 - 129.3 (17.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.2"
D38V2, continuous
D38V3, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED   137  69
  DEL PEAK 11(4Q22.1) WILD-TYPE 292  90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED    137   69
  DEL PEAK 11(4Q22.1) WILD-TYPE  292   90
        clus
vv       DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  COLON                          137                           292
  RECTUM                          69                            90
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 11(4Q22.1) MUTATED        25        0       11        56         2
  DEL PEAK 11(4Q22.1) WILD-TYPE      77        1       25       109         8
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4Q22.1) MUTATED           1         5         10         34
  DEL PEAK 11(4Q22.1) WILD-TYPE         2        21         12         42
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 11(4Q22.1) MUTATED           26       25         9         1
  DEL PEAK 11(4Q22.1) WILD-TYPE         26       35        16         0
D38V4, multiclass
            clus
vv           DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  STAGE I                             25                            77
  STAGE IA                             0                             1
  STAGE II                            11                            25
  STAGE IIA                           56                           109
  STAGE IIB                            2                             8
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                          10                            12
  STAGE IIIB                          34                            42
  STAGE IIIC                          26                            26
  STAGE IV                            25                            35
  STAGE IVA                            9                            16
  STAGE IVB                            1                             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                            T0+T1  T2  T3  T4
  DEL PEAK 11(4Q22.1) MUTATED       6  28 151  25
  DEL PEAK 11(4Q22.1) WILD-TYPE    14  77 252  37
D38V5, multiclass
       clus
vv      DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  T0+T1                           6                            14
  T2                             28                            77
  T3                            151                           252
  T4                             25                            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 11(4Q22.1) MUTATED    98  64  48
  DEL PEAK 11(4Q22.1) WILD-TYPE 237  82  60
D38V6, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  N0                          98                           237
  N1                          64                            82
  N2                          48                            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 11(4Q22.1) MUTATED   149  29   4   1  22
  DEL PEAK 11(4Q22.1) WILD-TYPE 294  43   5   0  36
D38V7, multiclass
     clus
vv    DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  M0                          149                           294
  M1                           29                            43
  M1A                           4                             5
  M1B                           1                             0
  MX                           22                            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"
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED    90 120
  DEL PEAK 11(4Q22.1) WILD-TYPE 187 195
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED     90  120
  DEL PEAK 11(4Q22.1) WILD-TYPE  187  195
        clus
vv       DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  FEMALE                          90                           187
  MALE                           120                           195
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 11(4Q22.1) MUTATED                    128
  DEL PEAK 11(4Q22.1) WILD-TYPE                  245
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(4Q22.1) MUTATED                               9
  DEL PEAK 11(4Q22.1) WILD-TYPE                            46
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 11(4Q22.1) MUTATED                      64
  DEL PEAK 11(4Q22.1) WILD-TYPE                    79
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(4Q22.1) MUTATED                                4
  DEL PEAK 11(4Q22.1) WILD-TYPE                              9
D38V9, multiclass
                                clus
vv                               DEL PEAK 11(4Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   128
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   64
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK 11(4Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     245
  COLON MUCINOUS ADENOCARCINOMA                             46
  RECTAL ADENOCARCINOMA                                     79
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D38V10, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q22.1) MUTATED     8 202
  DEL PEAK 11(4Q22.1) WILD-TYPE   1 381
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q22.1) MUTATED      8  202
  DEL PEAK 11(4Q22.1) WILD-TYPE    1  381
     clus
vv    DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  NO                            8                             1
  YES                         202                           381
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q22.1) MUTATED   154   2  12   7
  DEL PEAK 11(4Q22.1) WILD-TYPE 272   3  24  20
D38V11, multiclass
    clus
vv   DEL PEAK 11(4Q22.1) MUTATED DEL PEAK 11(4Q22.1) WILD-TYPE
  R0                         154                           272
  R1                           2                             3
  R2                          12                            24
  RX                           7                            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"
D38V12, 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     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(4Q22.1) MUTATED                          17   109
  DEL PEAK 11(4Q22.1) WILD-TYPE                        27   183
D38V13, multiclass
                                  clus
vv                                 DEL PEAK 11(4Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 17
  WHITE                                                    109
                                  clus
vv                                 DEL PEAK 11(4Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   27
  WHITE                                                      183
[1] 4 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 12(4Q35.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(4Q35.1) MUTATED   168  38
  DEL PEAK 12(4Q35.1) WILD-TYPE 289  68
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                          206                           357 
  DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE 
                           38                            68 
$`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-6196 TCGA-AY-A69D TCGA-AZ-4308 
       14.50        16.31         0.95         0.20         5.52        75.25 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5254 
        5.65         5.13        65.00        12.10        29.56         2.24 
TCGA-CA-5256 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-4752 
        2.14         0.10         1.35        48.20         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 
       29.06        22.03        22.98        30.08         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 
       15.02        17.03        14.04        29.03        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       11.01        11.08        11.01        14.99        13.51        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 
       17.75         1.32         7.92        17.85         7.53         9.04 
TCGA-D5-6929 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA 
       13.41        13.32       140.38         7.50        44.32       131.51 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 
        6.12        14.04        26.47        13.38         1.55        16.24 
TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6310 
       33.67        35.41         8.35        82.39        23.51        45.11 
TCGA-G4-6315 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV 
       36.72        91.79        46.75         4.11         5.98        26.99 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3587 
       37.74        10.39        14.50        15.39         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       34.03         6.05        19.99        29.98        32.98         0.99 
TCGA-AG-3883 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       13.94        25.97        23.01        12.00        70.03        64.01 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
       41.00         0.49         0.69        10.19         6.05         6.05 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        4.73        11.01        12.99        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6509 
       30.05       126.44       129.27        24.13         2.40        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 
       15.85        16.34        16.41        11.97         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6864 
       14.86         0.39         1.02         0.66         0.53         0.46 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`DEL PEAK 12(4Q35.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        37.02        46.65        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       44.91        16.04        36.53        14.53        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       30.44        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       27.09        22.52         8.38        25.18        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 
       20.12        19.66        16.24        24.92         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-3519 TCGA-AA-3520 TCGA-AA-3524 
        1.02        13.02         1.02         9.07        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 
        8.05        19.07        19.07        29.00        12.99         0.99 
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-3663 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
       13.94        61.02         6.97        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        19.00         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-3855 TCGA-AA-3858 
        1.02        17.98        15.95        14.93        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-3952 
       12.99        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       13.05        34.06        25.02        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-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-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        37.02        39.06        51.98 
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-A5EK TCGA-AM-5820 TCGA-AM-5821 
        1.58         0.10         0.76         0.43         0.46         0.92 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 
       27.09        15.75        21.44        17.82         5.19        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41        32.94        83.80        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6605 TCGA-AZ-6606 
       61.41        49.41         6.77       100.01         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         3.06         3.25         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.26         0.33        17.56       102.44        40.34        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        21.01         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-5860 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       27.02        16.01        15.02        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 
       21.99        14.99        12.99        14.04        12.95        13.05 
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-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       20.42        18.25        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-D5-6927 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-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
       12.59       135.65         7.76       139.17        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-F4-6461 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-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 
       29.59         1.28         0.53        19.43       107.67        28.21 
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-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       51.75        39.42        35.93        36.00        26.43        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-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 
        5.06         2.79         5.59        17.29        14.76        17.95 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
        8.45        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 
        8.02         7.07         2.01        24.00         1.02         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 
        0.99         1.02         0.99        19.99        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-4007 
       13.02        35.01        14.01         1.02        32.02         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 
       17.03         0.99        20.98         6.02        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 
       36.03         9.07         1.02        31.00        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       49.97         1.94        38.96        61.97        38.04         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        0.72         4.60         1.81         6.97         9.37        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
       60.03         7.99        10.98        15.02        12.00        13.97 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06         5.29        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       18.28        17.69        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6813 TCGA-F5-6861 
       13.64        17.46         8.45        37.51         0.69         1.12 
TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.76        55.76        47.08 

  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 
                        17.80                         17.95 
[1] "0.1 - 140.4 (17.8)" "0.1 - 139.2 (17.9)"
[1] "hr=" "1"  
D39V2, continuous
D39V3, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED   147  68
  DEL PEAK 12(4Q35.1) WILD-TYPE 282  91
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED    147   68
  DEL PEAK 12(4Q35.1) WILD-TYPE  282   91
        clus
vv       DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  COLON                          147                           282
  RECTUM                          68                            91
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 12(4Q35.1) MUTATED        29        0        9        60         1
  DEL PEAK 12(4Q35.1) WILD-TYPE      73        1       27       105         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(4Q35.1) MUTATED           1         9          9         31
  DEL PEAK 12(4Q35.1) WILD-TYPE         2        17         13         45
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 12(4Q35.1) MUTATED           28       28        10         0
  DEL PEAK 12(4Q35.1) WILD-TYPE         24       32        15         1
D39V4, multiclass
            clus
vv           DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  STAGE I                             29                            73
  STAGE IA                             0                             1
  STAGE II                             9                            27
  STAGE IIA                           60                           105
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            9                            17
  STAGE IIIA                           9                            13
  STAGE IIIB                          31                            45
  STAGE IIIC                          28                            24
  STAGE IV                            28                            32
  STAGE IVA                           10                            15
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 12(4Q35.1) MUTATED       7  32 158  22
  DEL PEAK 12(4Q35.1) WILD-TYPE    13  73 245  40
D39V5, multiclass
       clus
vv      DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  T0+T1                           7                            13
  T2                             32                            73
  T3                            158                           245
  T4                             22                            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 12(4Q35.1) MUTATED   104  63  52
  DEL PEAK 12(4Q35.1) WILD-TYPE 231  83  56
D39V6, multiclass
    clus
vv   DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  N0                         104                           231
  N1                          63                            83
  N2                          52                            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 12(4Q35.1) MUTATED   157  33   5   0  21
  DEL PEAK 12(4Q35.1) WILD-TYPE 286  39   4   1  37
D39V7, multiclass
     clus
vv    DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  M0                          157                           286
  M1                           33                            39
  M1A                           5                             4
  M1B                           0                             1
  MX                           21                            37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED   104 115
  DEL PEAK 12(4Q35.1) WILD-TYPE 173 200
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED    104  115
  DEL PEAK 12(4Q35.1) WILD-TYPE  173  200
        clus
vv       DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  FEMALE                         104                           173
  MALE                           115                           200
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 12(4Q35.1) MUTATED                    134
  DEL PEAK 12(4Q35.1) WILD-TYPE                  239
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 12(4Q35.1) MUTATED                              13
  DEL PEAK 12(4Q35.1) WILD-TYPE                            42
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 12(4Q35.1) MUTATED                      64
  DEL PEAK 12(4Q35.1) WILD-TYPE                    79
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 12(4Q35.1) MUTATED                                3
  DEL PEAK 12(4Q35.1) WILD-TYPE                             10
D39V9, multiclass
                                clus
vv                               DEL PEAK 12(4Q35.1) MUTATED
  COLON ADENOCARCINOMA                                   134
  COLON MUCINOUS ADENOCARCINOMA                           13
  RECTAL ADENOCARCINOMA                                   64
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK 12(4Q35.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     239
  COLON MUCINOUS ADENOCARCINOMA                             42
  RECTAL ADENOCARCINOMA                                     79
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, binary
                               cls
clus                              0   1
  DEL PEAK 12(4Q35.1) MUTATED     8 211
  DEL PEAK 12(4Q35.1) WILD-TYPE   1 372
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(4Q35.1) MUTATED      8  211
  DEL PEAK 12(4Q35.1) WILD-TYPE    1  372
     clus
vv    DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  NO                            8                             1
  YES                         211                           372
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(4Q35.1) MUTATED   157   1  15   8
  DEL PEAK 12(4Q35.1) WILD-TYPE 269   4  21  19
D39V11, multiclass
    clus
vv   DEL PEAK 12(4Q35.1) MUTATED DEL PEAK 12(4Q35.1) WILD-TYPE
  R0                         157                           269
  R1                           1                             4
  R2                          15                            21
  RX                           8                            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"
D39V12, 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     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(4Q35.1) MUTATED                          19   109
  DEL PEAK 12(4Q35.1) WILD-TYPE                        25   183
D39V13, multiclass
                                  clus
vv                                 DEL PEAK 12(4Q35.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 19
  WHITE                                                    109
                                  clus
vv                                 DEL PEAK 12(4Q35.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   25
  WHITE                                                      183
[1] 4 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 13(5Q11.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q11.2) MUTATED   106  33
  DEL PEAK 13(5Q11.2) WILD-TYPE 351  73
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                          139                           424 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                           33                            73 
$`DEL PEAK 13(5Q11.2) 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-QG-A5YV TCGA-AF-2687 TCGA-AF-2690 
       36.00        91.79         4.11        26.99        24.13        17.23 
TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3728 
       43.04        37.74        10.39        15.39        10.39        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 
        1.02        32.98        19.99        17.03         1.02        48.03 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00Y TCGA-AG-A01W TCGA-AG-A01Y 
       28.04        36.03        17.03        23.01        70.03        64.01 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-BM-6198 TCGA-CI-6620 TCGA-CL-5918 
        1.94        38.96        41.00        10.19         6.05         7.99 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DY-A0XA 
       12.99        13.97        15.02        36.00         7.10       126.44 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 
       57.24       129.27        51.48        20.55        16.41        13.64 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-G5-6233 
       11.97         8.45        37.51        14.86         1.02        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 13(5Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
        5.06        46.65        17.79        42.28        44.91        35.11 
TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       45.60        37.05        37.25        32.45        32.91        31.63 
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-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6653 TCGA-A6-6780 
       22.52        24.13         8.38        20.61        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-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3506 
        1.02         3.02         1.02        37.05         1.02        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-3543 TCGA-AA-3544 
       19.07        34.03        29.00        29.00         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        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-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 
       54.02         2.01        14.01         0.92        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 
       11.01         5.98        36.00         5.03        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-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       15.95        38.99        14.93        17.03         0.99        36.03 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
       32.05        53.00        17.03        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-3971 TCGA-AA-3972 TCGA-AA-3973 
       24.00        20.98        34.03        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-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05        17.03         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       14.99        21.99        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-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-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-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-6964 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        0.72         1.58         0.76         0.43         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       14.50        27.09         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-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-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10       100.01        11.74         3.19         2.24 
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-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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.01         2.93         2.01       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-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       12.00        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-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-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        15.12         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       15.58        12.39        14.30         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-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
      140.38         7.50       135.65         7.76       139.17        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-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18        13.38        11.11        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
        6.18        35.87        16.31        29.59        16.24         1.28 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 
        0.53        35.41        19.43       107.67        28.21        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-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6321 
       51.75        39.42        35.93        36.72        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YX 
       52.80         5.06         2.79         5.98         5.59        17.29 
TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       14.76        17.95        13.55        19.10        12.72        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
        8.45        20.02        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
       15.95        19.99        19.99         7.99         0.99         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       32.02        19.99        14.04         1.02         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        12.00        31.00        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       49.97        61.97        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        0.72         4.60         1.81         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03        10.98        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       12.00        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       41.36        24.13        32.61         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-F5-6464 
       16.31         8.61        11.51        10.78        17.46         9.96 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       31.30         0.39         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.76         0.46        55.76        47.08 

  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                       131.51                        140.38 
  DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE 
                        20.55                         17.51 
[1] "0.1 - 131.5 (20.6)" "0.1 - 140.4 (17.5)"
[1] "hr=" "1.3"
D40V2, continuous
D40V3, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q11.2) MUTATED    96  51
  DEL PEAK 13(5Q11.2) WILD-TYPE 333 108
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q11.2) MUTATED     96   51
  DEL PEAK 13(5Q11.2) WILD-TYPE  333  108
        clus
vv       DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  COLON                           96                           333
  RECTUM                          51                           108
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 13(5Q11.2) MUTATED        22        0        7        32         1
  DEL PEAK 13(5Q11.2) WILD-TYPE      80        1       29       133         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(5Q11.2) MUTATED           1         5          9         16
  DEL PEAK 13(5Q11.2) WILD-TYPE         2        21         13         60
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 13(5Q11.2) MUTATED           19       19        12         0
  DEL PEAK 13(5Q11.2) WILD-TYPE         33       41        13         1
D40V4, multiclass
            clus
vv           DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  STAGE I                             22                            80
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           32                           133
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            5                            21
  STAGE IIIA                           9                            13
  STAGE IIIB                          16                            60
  STAGE IIIC                          19                            33
  STAGE IV                            19                            41
  STAGE IVA                           12                            13
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 13(5Q11.2) MUTATED       5  26 101  15
  DEL PEAK 13(5Q11.2) WILD-TYPE    15  79 302  47
D40V5, multiclass
       clus
vv      DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  T0+T1                           5                            15
  T2                             26                            79
  T3                            101                           302
  T4                             15                            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 13(5Q11.2) MUTATED    68  42  37
  DEL PEAK 13(5Q11.2) WILD-TYPE 267 104  71
D40V6, multiclass
    clus
vv   DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  N0                          68                           267
  N1                          42                           104
  N2                          37                            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 13(5Q11.2) MUTATED    98  24   5   0  18
  DEL PEAK 13(5Q11.2) WILD-TYPE 345  48   4   1  40
D40V7, multiclass
     clus
vv    DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  M0                           98                           345
  M1                           24                            48
  M1A                           5                             4
  M1B                           0                             1
  MX                           18                            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"
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q11.2) MUTATED    67  80
  DEL PEAK 13(5Q11.2) WILD-TYPE 210 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q11.2) MUTATED     67   80
  DEL PEAK 13(5Q11.2) WILD-TYPE  210  235
        clus
vv       DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  FEMALE                          67                           210
  MALE                            80                           235
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 13(5Q11.2) MUTATED                     90
  DEL PEAK 13(5Q11.2) WILD-TYPE                  283
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 13(5Q11.2) MUTATED                               6
  DEL PEAK 13(5Q11.2) WILD-TYPE                            49
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 13(5Q11.2) MUTATED                      48
  DEL PEAK 13(5Q11.2) WILD-TYPE                    95
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 13(5Q11.2) MUTATED                                2
  DEL PEAK 13(5Q11.2) WILD-TYPE                             11
D40V9, multiclass
                                clus
vv                               DEL PEAK 13(5Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    90
  COLON MUCINOUS ADENOCARCINOMA                            6
  RECTAL ADENOCARCINOMA                                   48
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 13(5Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     283
  COLON MUCINOUS ADENOCARCINOMA                             49
  RECTAL ADENOCARCINOMA                                     95
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D40V10, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q11.2) MUTATED     8 139
  DEL PEAK 13(5Q11.2) WILD-TYPE   1 444
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q11.2) MUTATED      8  139
  DEL PEAK 13(5Q11.2) WILD-TYPE    1  444
     clus
vv    DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  NO                            8                             1
  YES                         139                           444
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q11.2) MUTATED    99   2   9   5
  DEL PEAK 13(5Q11.2) WILD-TYPE 327   3  27  22
D40V11, multiclass
    clus
vv   DEL PEAK 13(5Q11.2) MUTATED DEL PEAK 13(5Q11.2) WILD-TYPE
  R0                          99                           327
  R1                           2                             3
  R2                           9                            27
  RX                           5                            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"
D40V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(5Q11.2) MUTATED                                  1     2
  DEL PEAK 13(5Q11.2) WILD-TYPE                                0    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(5Q11.2) MUTATED                          11    79
  DEL PEAK 13(5Q11.2) WILD-TYPE                        33   213
D40V13, multiclass
                                  clus
vv                                 DEL PEAK 13(5Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                 11
  WHITE                                                     79
                                  clus
vv                                 DEL PEAK 13(5Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   33
  WHITE                                                      213
[1] 4 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 14(5Q22.2) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q22.2) MUTATED   125  41
  DEL PEAK 14(5Q22.2) WILD-TYPE 332  65
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          166                           397 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                           41                            65 
$`DEL PEAK 14(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-QG-A5YV TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 
        4.11        26.99        24.13        17.23        43.04        37.74 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3612 TCGA-AG-3728 
       10.39        15.39        10.39        32.02        19.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 
        1.02        32.98        19.99        17.03         1.02        48.03 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A01L 
       28.04        36.03        17.03         6.02        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6903 
       70.03        64.01         1.94        38.96        41.00         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       10.19         6.05         7.99        12.99        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       36.00         7.10        13.05       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6881 
       51.48        20.55        19.96        18.28        16.34        16.41 
TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6233 
        9.96        14.86         0.46        18.28 

$`DEL PEAK 14(5Q22.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 
       44.91        35.11        45.60        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-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 
       22.06        32.71        29.16        22.52         8.38        20.61 
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-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       24.92        61.84        52.44         1.02         3.02        37.05 
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-3524 TCGA-AA-3525 
       38.99         1.02         9.07        24.03        36.03         8.05 
TCGA-AA-3526 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3544 
       19.07        34.03        29.00        29.00         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       33.99        21.01        17.95        29.95        23.01        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-3680 TCGA-AA-3681 
        2.01        14.01         0.92        47.05        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3715 TCGA-AA-3812 
       37.05        36.00         5.03        26.99         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-3844 TCGA-AA-3846 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 
       14.93        17.03        36.03        32.05        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-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-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-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       24.00        27.02         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-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-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-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       51.98        39.98         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-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        0.72         1.58         0.43         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       27.09         0.95        15.75        17.82         5.19         5.52 
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-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       22.36        61.41        49.41        12.10       100.01        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        3.19         2.24         3.06         3.25         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-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.01         2.93         2.01 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5348 
       23.05        20.02        37.02        27.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 
       30.08        16.01        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       12.00        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-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-D5-5540 TCGA-D5-5541 
       10.06        12.03        14.99        12.26        13.51        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       20.19        20.42        17.75        18.25         1.32         7.92 
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-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.39        14.30         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-A1D6 
       10.26       119.70        24.43        38.20       130.65        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       13.32        12.59         7.50       131.51       135.65       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6461 
       14.04        81.37       119.93        35.97        95.18        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         5.06         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
        5.59        17.29        14.76        17.95        13.55        19.10 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       12.72        14.50         8.45        20.02        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
        0.99        15.95        19.99         7.99         0.99         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       32.02        19.99        14.04         1.02         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       13.94        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
        1.02        31.00        10.98        51.98        49.97        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 
       10.98        11.01        15.02        12.00        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
       10.06         5.29       129.27        24.13        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
        2.40        20.91        17.00        15.85        17.69        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45        37.51        31.30         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.53         1.12         0.76        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                        18.64                         17.79 
[1] "0.1 - 140.4 (18.6)" "0.1 - 139.2 (17.8)"
[1] "hr=" "1.4"
D41V2, continuous
D41V3, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   121  57
  DEL PEAK 14(5Q22.2) WILD-TYPE 308 102
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    121   57
  DEL PEAK 14(5Q22.2) WILD-TYPE  308  102
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  COLON                          121                           308
  RECTUM                          57                           102
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 14(5Q22.2) MUTATED        25        0        9        43         0
  DEL PEAK 14(5Q22.2) WILD-TYPE      77        1       27       122        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q22.2) MUTATED           1         6          9         24
  DEL PEAK 14(5Q22.2) WILD-TYPE         2        20         13         52
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 14(5Q22.2) MUTATED           21       23        12         0
  DEL PEAK 14(5Q22.2) WILD-TYPE         31       37        13         1
D41V4, multiclass
            clus
vv           DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  STAGE I                             25                            77
  STAGE IA                             0                             1
  STAGE II                             9                            27
  STAGE IIA                           43                           122
  STAGE IIB                            0                            10
  STAGE IIC                            1                             2
  STAGE III                            6                            20
  STAGE IIIA                           9                            13
  STAGE IIIB                          24                            52
  STAGE IIIC                          21                            31
  STAGE IV                            23                            37
  STAGE IVA                           12                            13
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 14(5Q22.2) MUTATED       4  30 126  18
  DEL PEAK 14(5Q22.2) WILD-TYPE    16  75 277  44
D41V5, multiclass
       clus
vv      DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  T0+T1                           4                            16
  T2                             30                            75
  T3                            126                           277
  T4                             18                            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 14(5Q22.2) MUTATED    86  51  41
  DEL PEAK 14(5Q22.2) WILD-TYPE 249  95  67
D41V6, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  N0                          86                           249
  N1                          51                            95
  N2                          41                            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 14(5Q22.2) MUTATED   121  27   6   0  20
  DEL PEAK 14(5Q22.2) WILD-TYPE 322  45   3   1  38
D41V7, multiclass
     clus
vv    DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  M0                          121                           322
  M1                           27                            45
  M1A                           6                             3
  M1B                           0                             1
  MX                           20                            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"
D41V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED    79  99
  DEL PEAK 14(5Q22.2) WILD-TYPE 198 216
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED     79   99
  DEL PEAK 14(5Q22.2) WILD-TYPE  198  216
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  FEMALE                          79                           198
  MALE                            99                           216
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                    111
  DEL PEAK 14(5Q22.2) WILD-TYPE                  262
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                              10
  DEL PEAK 14(5Q22.2) WILD-TYPE                            45
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                      54
  DEL PEAK 14(5Q22.2) WILD-TYPE                    89
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                                2
  DEL PEAK 14(5Q22.2) WILD-TYPE                             11
D41V9, multiclass
                                clus
vv                               DEL PEAK 14(5Q22.2) MUTATED
  COLON ADENOCARCINOMA                                   111
  COLON MUCINOUS ADENOCARCINOMA                           10
  RECTAL ADENOCARCINOMA                                   54
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 14(5Q22.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     262
  COLON MUCINOUS ADENOCARCINOMA                             45
  RECTAL ADENOCARCINOMA                                     89
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D41V10, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED     8 170
  DEL PEAK 14(5Q22.2) WILD-TYPE   1 413
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED      8  170
  DEL PEAK 14(5Q22.2) WILD-TYPE    1  413
     clus
vv    DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  NO                            8                             1
  YES                         170                           413
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q22.2) MUTATED   115   2  15   7
  DEL PEAK 14(5Q22.2) WILD-TYPE 311   3  21  20
D41V11, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  R0                         115                           311
  R1                           2                             3
  R2                          15                            21
  RX                           7                            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"
D41V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(5Q22.2) MUTATED                                  1     3
  DEL PEAK 14(5Q22.2) WILD-TYPE                                0     9
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(5Q22.2) MUTATED                          10    93
  DEL PEAK 14(5Q22.2) WILD-TYPE                        34   199
D41V13, multiclass
                                  clus
vv                                 DEL PEAK 14(5Q22.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 10
  WHITE                                                     93
                                  clus
vv                                 DEL PEAK 14(5Q22.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        9
  BLACK OR AFRICAN AMERICAN                                   34
  WHITE                                                      199
[1] 4 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 15(6P25.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(6P25.3) MUTATED    55  16
  DEL PEAK 15(6P25.3) WILD-TYPE 402  90
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           71                           492 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                           16                            90 
$`DEL PEAK 15(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 TCGA-AF-2690 
       13.32        26.47       117.07        33.67        36.00        17.23 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3584 TCGA-AG-3593 
       13.55        19.10        12.72        14.50        24.00        34.03 
TCGA-AG-3598 TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A011 TCGA-BM-6198 TCGA-DC-4745 
       50.04        36.03        13.94        37.02        10.19        10.98 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6511 TCGA-EI-6883 
       13.05         5.29        24.13        15.85        11.51 

$`DEL PEAK 15(6P25.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        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-A6-2684 
       42.28        44.91        35.11        45.60        13.94        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        36.53        14.53        32.45        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-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        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-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-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         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-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3664 
       20.98        19.99        19.99        78.08         6.05        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-3696 TCGA-AA-3697 TCGA-AA-3710 
       11.01         5.98        19.00         5.03        85.05        26.99 
TCGA-AA-3713 TCGA-AA-3811 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-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        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-3866 
       33.07        36.03        32.05         0.99        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       24.03        27.02        31.00         2.01        33.01        26.01 
TCGA-AA-3950 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-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-3994 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07         7.96        27.02        38.04        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        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-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
        0.99        32.02        12.00        31.00        31.00         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 
       35.01         1.02        33.04        35.01        37.02        39.06 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R 
       51.98         2.96        39.98         2.01         5.03        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-6901 TCGA-AD-6963 TCGA-AD-6965 
        4.21        56.55         0.79         1.02         0.10         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-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-4615 TCGA-AZ-4616 
       75.25        50.37        58.39         1.41        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-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-6608 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        1.94         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        21.01         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-5344 TCGA-CM-5349 
       26.04         8.02        27.02        13.02        22.03        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-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        12.00        14.04        29.03        16.04        21.99 
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-6679 TCGA-CM-6680 TCGA-D5-5538 
       12.95        13.05        11.08        10.06        12.03        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-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        15.12         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-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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-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-A28C 
      135.65         7.76       139.17         6.12        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
      119.93        35.97        60.79        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-F4-6809 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-G4-6295 TCGA-G4-6297 
       35.41        19.43       107.67        28.21         8.35        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-G4-6314 TCGA-G4-6315 
       55.04        51.75        45.11        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-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       91.79        46.75        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       24.13        17.95        43.04        37.74        10.39         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07         1.02         2.01         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       20.98         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03         7.99        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                         0.43                          0.07 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       117.07                        140.38 
  DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE 
                       17.230                        18.015 
[1] "0.4 - 117.1 (17.2)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.5"
D42V2, continuous
D42V3, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    54  21
  DEL PEAK 15(6P25.3) WILD-TYPE 375 138
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     54   21
  DEL PEAK 15(6P25.3) WILD-TYPE  375  138
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  COLON                           54                           375
  RECTUM                          21                           138
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 15(6P25.3) MUTATED         9        0        7        27         1
  DEL PEAK 15(6P25.3) WILD-TYPE      93        1       29       138         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(6P25.3) MUTATED           1         4          2          6
  DEL PEAK 15(6P25.3) WILD-TYPE         2        22         20         70
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 15(6P25.3) MUTATED            7        7         5         0
  DEL PEAK 15(6P25.3) WILD-TYPE         45       53        20         1
D42V4, multiclass
            clus
vv           DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  STAGE I                              9                            93
  STAGE IA                             0                             1
  STAGE II                             7                            29
  STAGE IIA                           27                           138
  STAGE IIB                            1                             9
  STAGE IIC                            1                             2
  STAGE III                            4                            22
  STAGE IIIA                           2                            20
  STAGE IIIB                           6                            70
  STAGE IIIC                           7                            45
  STAGE IV                             7                            53
  STAGE IVA                            5                            20
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 15(6P25.3) MUTATED       2   9  57  10
  DEL PEAK 15(6P25.3) WILD-TYPE    18  96 346  52
D42V5, multiclass
       clus
vv      DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  T0+T1                           2                            18
  T2                              9                            96
  T3                             57                           346
  T4                             10                            52
[1] 4 2
[1] TRUE
[1] "dimension 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(6P25.3) MUTATED    48  15  15
  DEL PEAK 15(6P25.3) WILD-TYPE 287 131  93
D42V6, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  N0                          48                           287
  N1                          15                           131
  N2                          15                            93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 15(6P25.3) MUTATED    55   8   3   0  10
  DEL PEAK 15(6P25.3) WILD-TYPE 388  64   6   1  48
D42V7, multiclass
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  M0                           55                           388
  M1                            8                            64
  M1A                           3                             6
  M1B                           0                             1
  MX                           10                            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"
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED    29  49
  DEL PEAK 15(6P25.3) WILD-TYPE 248 266
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED     29   49
  DEL PEAK 15(6P25.3) WILD-TYPE  248  266
        clus
vv       DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  FEMALE                          29                           248
  MALE                            49                           266
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                     49
  DEL PEAK 15(6P25.3) WILD-TYPE                  324
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                               5
  DEL PEAK 15(6P25.3) WILD-TYPE                            50
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                      18
  DEL PEAK 15(6P25.3) WILD-TYPE                   125
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(6P25.3) MUTATED                                3
  DEL PEAK 15(6P25.3) WILD-TYPE                             10
D42V9, multiclass
                                clus
vv                               DEL PEAK 15(6P25.3) MUTATED
  COLON ADENOCARCINOMA                                    49
  COLON MUCINOUS ADENOCARCINOMA                            5
  RECTAL ADENOCARCINOMA                                   18
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK 15(6P25.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     324
  COLON MUCINOUS ADENOCARCINOMA                             50
  RECTAL ADENOCARCINOMA                                    125
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, binary
                               cls
clus                              0   1
  DEL PEAK 15(6P25.3) MUTATED     2  76
  DEL PEAK 15(6P25.3) WILD-TYPE   7 507
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(6P25.3) MUTATED      2   76
  DEL PEAK 15(6P25.3) WILD-TYPE    7  507
     clus
vv    DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  NO                            2                             7
  YES                          76                           507
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(6P25.3) MUTATED    55   0   3   6
  DEL PEAK 15(6P25.3) WILD-TYPE 371   5  33  21
D42V11, multiclass
    clus
vv   DEL PEAK 15(6P25.3) MUTATED DEL PEAK 15(6P25.3) WILD-TYPE
  R0                          55                           371
  R1                           0                             5
  R2                           3                            33
  RX                           6                            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"
D42V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(6P25.3) MUTATED                                  0     4
  DEL PEAK 15(6P25.3) WILD-TYPE                                1     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(6P25.3) MUTATED                           1    38
  DEL PEAK 15(6P25.3) WILD-TYPE                        43   254
D42V13, multiclass
                                  clus
vv                                 DEL PEAK 15(6P25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     38
                                  clus
vv                                 DEL PEAK 15(6P25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   43
  WHITE                                                      254
[1] 4 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 16(6Q26) MUTATION ANALYSIS
D43V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 16(6Q26) MUTATED    63  21
  DEL PEAK 16(6Q26) WILD-TYPE 394  85
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         84                         479 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                         21                          85 
$`DEL PEAK 16(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-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
        0.20         5.13        49.41         3.19         2.24         3.06 
TCGA-CA-5256 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 
        2.14        11.01        13.05        11.08        11.01        14.99 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-D5-6898 TCGA-DM-A1D7 TCGA-DM-A1HA 
       20.19        17.75        15.12         7.53        13.32       131.51 
TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6297 TCGA-NH-A6GA TCGA-AF-2690 TCGA-AF-2691 
        1.55        33.67        82.39         5.98        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AG-3575 TCGA-AG-3578 
       13.55        19.10        12.72        37.74        12.00        32.02 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 
       24.00        46.03        34.03         2.01         6.05        19.99 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A011 TCGA-AH-6544 TCGA-AH-6644 
       14.04         1.02        13.94        37.02         0.49         0.72 
TCGA-CI-6623 TCGA-DC-6682 TCGA-DT-5265 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
        9.37        13.05         5.29         0.76        18.28        26.43 

$`DEL PEAK 16(6Q26) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        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-A6-5656 TCGA-A6-5657 
       16.04        34.65        36.53        14.53        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-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       32.71        29.16        27.09        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       20.12        19.66        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-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-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3667 
       13.94        19.99        78.08         6.05         6.97        14.01 
TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
        0.92        50.04        47.05        47.01        15.02         5.98 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3811 TCGA-AA-3812 
       19.00         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-3842 
        0.99        25.02         1.02        17.98        15.95        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-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-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00         2.01        33.01        26.01        24.00        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-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-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        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-A024 TCGA-AA-A029 
       35.01         1.02        35.01        37.02        39.06        51.98 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         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-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 
        0.79         0.72         1.02         0.10         0.76         0.20 
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-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-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-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6603 
       62.79        61.41         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 
       21.01         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-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-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        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-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6679 
       13.02        15.02        14.04        12.95        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-D5-6536 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-D5-6920 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-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-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-F4-6461 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-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       13.45         6.18        35.87        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-G4-6298 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-G4-6310 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-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        4.11         5.06         2.79         5.59        26.99        17.29 
TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       14.76        24.13        17.95        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 
       15.39        20.02        10.39        36.03         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02         2.01         1.02        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4022 
       32.02        19.99        28.04        36.03        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       20.98         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.04         1.45         0.69         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       12.95        10.06       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.46        55.76        47.08 

  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                       0.20                        0.07 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                     131.51                      140.38 
  DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE 
                     15.055                      18.250 
[1] "0.2 - 131.5 (15.1)" "0.1 - 140.4 (18.2)"
[1] "hr=" "1.7"
D43V2, continuous
D43V3, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    60  28
  DEL PEAK 16(6Q26) WILD-TYPE 369 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     60   28
  DEL PEAK 16(6Q26) WILD-TYPE  369  131
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  COLON                         60                         369
  RECTUM                        28                         131
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 16(6Q26) MUTATED        13        0        8        19         1
  DEL PEAK 16(6Q26) WILD-TYPE      89        1       28       146         9
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6Q26) MUTATED           1         4          2         10
  DEL PEAK 16(6Q26) WILD-TYPE         2        22         20         66
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 16(6Q26) MUTATED           14       12         3         1
  DEL PEAK 16(6Q26) WILD-TYPE         38       48        22         0
D43V4, multiclass
            clus
vv           DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  STAGE I                           13                          89
  STAGE IA                           0                           1
  STAGE II                           8                          28
  STAGE IIA                         19                         146
  STAGE IIB                          1                           9
  STAGE IIC                          1                           2
  STAGE III                          4                          22
  STAGE IIIA                         2                          20
  STAGE IIIB                        10                          66
  STAGE IIIC                        14                          38
  STAGE IV                          12                          48
  STAGE IVA                          3                          22
  STAGE IVB                          1                           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                          T0+T1  T2  T3  T4
  DEL PEAK 16(6Q26) MUTATED       5  10  63  12
  DEL PEAK 16(6Q26) WILD-TYPE    15  95 340  50
D43V5, multiclass
       clus
vv      DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  T0+T1                         5                          15
  T2                           10                          95
  T3                           63                         340
  T4                           12                          50
[1] 4 2
[1] TRUE
[1] "dimension 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(6Q26) MUTATED    43  18  28
  DEL PEAK 16(6Q26) WILD-TYPE 292 128  80
D43V6, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  N0                        43                         292
  N1                        18                         128
  N2                        28                          80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK 16(6Q26) MUTATED    59  14   2   1  13
  DEL PEAK 16(6Q26) WILD-TYPE 384  58   7   0  45
D43V7, multiclass
     clus
vv    DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  M0                         59                         384
  M1                         14                          58
  M1A                         2                           7
  M1B                         1                           0
  MX                         13                          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"
D43V8, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED    37  53
  DEL PEAK 16(6Q26) WILD-TYPE 240 262
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED     37   53
  DEL PEAK 16(6Q26) WILD-TYPE  240  262
        clus
vv       DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  FEMALE                        37                         240
  MALE                          53                         262
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                     52
  DEL PEAK 16(6Q26) WILD-TYPE                  321
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                               8
  DEL PEAK 16(6Q26) WILD-TYPE                            47
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                      22
  DEL PEAK 16(6Q26) WILD-TYPE                   121
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(6Q26) MUTATED                                6
  DEL PEAK 16(6Q26) WILD-TYPE                              7
D43V9, multiclass
                                clus
vv                               DEL PEAK 16(6Q26) MUTATED
  COLON ADENOCARCINOMA                                  52
  COLON MUCINOUS ADENOCARCINOMA                          8
  RECTAL ADENOCARCINOMA                                 22
  RECTAL MUCINOUS ADENOCARCINOMA                         6
                                clus
vv                               DEL PEAK 16(6Q26) WILD-TYPE
  COLON ADENOCARCINOMA                                   321
  COLON MUCINOUS ADENOCARCINOMA                           47
  RECTAL ADENOCARCINOMA                                  121
  RECTAL MUCINOUS ADENOCARCINOMA                           7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, binary
                             cls
clus                            0   1
  DEL PEAK 16(6Q26) MUTATED     2  88
  DEL PEAK 16(6Q26) WILD-TYPE   7 495
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 16(6Q26) MUTATED      2   88
  DEL PEAK 16(6Q26) WILD-TYPE    7  495
     clus
vv    DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  NO                          2                           7
  YES                        88                         495
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 16(6Q26) MUTATED    60   1   8   7
  DEL PEAK 16(6Q26) WILD-TYPE 366   4  28  20
D43V11, multiclass
    clus
vv   DEL PEAK 16(6Q26) MUTATED DEL PEAK 16(6Q26) WILD-TYPE
  R0                        60                         366
  R1                         1                           4
  R2                         8                          28
  RX                         7                          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"
D43V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(6Q26) MUTATED                                  1     4
  DEL PEAK 16(6Q26) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(6Q26) MUTATED                           4    39
  DEL PEAK 16(6Q26) WILD-TYPE                        40   253
D43V13, multiclass
                                  clus
vv                                 DEL PEAK 16(6Q26) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                                4
  WHITE                                                   39
                                  clus
vv                                 DEL PEAK 16(6Q26) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 40
  WHITE                                                    253
[1] 4 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 17(7Q31.1) MUTATION ANALYSIS
D44V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(7Q31.1) MUTATED    12   2
  DEL PEAK 17(7Q31.1) WILD-TYPE 445 104
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                           14                           549 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                            2                           104 
$`DEL PEAK 17(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 TCGA-AG-3600 
       22.03         5.03        15.02        11.38        24.43         6.05 
TCGA-AG-A008 TCGA-DC-6682 
       13.94        13.05 

$`DEL PEAK 17(7Q31.1) 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-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 
       15.52        37.05        37.25        16.04        36.53        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-A6-6651 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-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-3552 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       21.01        13.02        24.00        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       20.98        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 
        6.05         6.97        54.02         2.01        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
       37.05        19.00        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-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-3855 
       14.93        17.03         0.99        33.07        36.03        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-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-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-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-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-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02         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-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       40.96         0.07         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-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.46         0.92        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
        0.20        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-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-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-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        21.01         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-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.98        30.08        16.01        15.02 
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-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
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-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        12.00        10.26       119.70        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-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        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-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       51.75        45.11        39.42        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-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       91.79        46.75        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         0.99        20.98         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                         5.03                          0.07 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                        35.01                        140.38 
  DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE 
                       16.025                        17.950 
[1] "5.0 - 35.0 (16.0)"  "0.1 - 140.4 (17.9)"
[1] "hr=" "1"  
D44V2, continuous
D44V3, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED    12   4
  DEL PEAK 17(7Q31.1) WILD-TYPE 417 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED     12    4
  DEL PEAK 17(7Q31.1) WILD-TYPE  417  155
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  COLON                           12                           417
  RECTUM                           4                           155
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 17(7Q31.1) MUTATED         3        0        0         7         0
  DEL PEAK 17(7Q31.1) WILD-TYPE      99        1       36       158        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(7Q31.1) MUTATED           0         1          1          1
  DEL PEAK 17(7Q31.1) WILD-TYPE         3        25         21         75
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 17(7Q31.1) MUTATED            2        0         1         0
  DEL PEAK 17(7Q31.1) WILD-TYPE         50       60        24         1
D44V4, multiclass
            clus
vv           DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  STAGE I                              3                            99
  STAGE IA                             0                             1
  STAGE II                             0                            36
  STAGE IIA                            7                           158
  STAGE IIB                            0                            10
  STAGE IIC                            0                             3
  STAGE III                            1                            25
  STAGE IIIA                           1                            21
  STAGE IIIB                           1                            75
  STAGE IIIC                           2                            50
  STAGE IV                             0                            60
  STAGE IVA                            1                            24
  STAGE IVB                            0                             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                            T0+T1  T2  T3  T4
  DEL PEAK 17(7Q31.1) MUTATED       0   4  12   0
  DEL PEAK 17(7Q31.1) WILD-TYPE    20 101 391  62
D44V5, multiclass
       clus
vv      DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  T0+T1                           0                            20
  T2                              4                           101
  T3                             12                           391
  T4                              0                            62
[1] 4 2
[1] TRUE
[1] "dimension 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(7Q31.1) MUTATED    10   3   3
  DEL PEAK 17(7Q31.1) WILD-TYPE 325 143 105
D44V6, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  N0                          10                           325
  N1                           3                           143
  N2                           3                           105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 17(7Q31.1) MUTATED    15   0   1   0   0
  DEL PEAK 17(7Q31.1) WILD-TYPE 428  72   8   1  58
D44V7, multiclass
     clus
vv    DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  M0                           15                           428
  M1                            0                            72
  M1A                           1                             8
  M1B                           0                             1
  MX                            0                            58
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V8, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED     9   7
  DEL PEAK 17(7Q31.1) WILD-TYPE 268 308
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      9    7
  DEL PEAK 17(7Q31.1) WILD-TYPE  268  308
        clus
vv       DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  FEMALE                           9                           268
  MALE                             7                           308
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                     11
  DEL PEAK 17(7Q31.1) WILD-TYPE                  362
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                               1
  DEL PEAK 17(7Q31.1) WILD-TYPE                            54
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                       3
  DEL PEAK 17(7Q31.1) WILD-TYPE                   140
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(7Q31.1) MUTATED                                1
  DEL PEAK 17(7Q31.1) WILD-TYPE                             12
D44V9, multiclass
                                clus
vv                               DEL PEAK 17(7Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    11
  COLON MUCINOUS ADENOCARCINOMA                            1
  RECTAL ADENOCARCINOMA                                    3
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 17(7Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     362
  COLON MUCINOUS ADENOCARCINOMA                             54
  RECTAL ADENOCARCINOMA                                    140
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D44V10, binary
                               cls
clus                              0   1
  DEL PEAK 17(7Q31.1) MUTATED     0  16
  DEL PEAK 17(7Q31.1) WILD-TYPE   9 567
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(7Q31.1) MUTATED      0   16
  DEL PEAK 17(7Q31.1) WILD-TYPE    9  567
     clus
vv    DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  NO                            0                             9
  YES                          16                           567
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 17(7Q31.1) MUTATED    15   0   0   0
  DEL PEAK 17(7Q31.1) WILD-TYPE 411   5  36  27
D44V11, multiclass
    clus
vv   DEL PEAK 17(7Q31.1) MUTATED DEL PEAK 17(7Q31.1) WILD-TYPE
  R0                          15                           411
  R1                           0                             5
  R2                           0                            36
  RX                           0                            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"
D44V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(7Q31.1) MUTATED                                  0     0
  DEL PEAK 17(7Q31.1) WILD-TYPE                                1    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(7Q31.1) MUTATED                           0    10
  DEL PEAK 17(7Q31.1) WILD-TYPE                        44   282
D44V13, multiclass
                                  clus
vv                                 DEL PEAK 17(7Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     10
                                  clus
vv                                 DEL PEAK 17(7Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   44
  WHITE                                                      282
[1] 4 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 18(8P23.2) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(8P23.2) MUTATED   215  52
  DEL PEAK 18(8P23.2) WILD-TYPE 242  54
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                          267                           296 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                           52                            54 
$`DEL PEAK 18(8P23.2) 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-A6-5662 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       31.63        29.19        23.61        29.16        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.08        25.18        20.61        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 
       61.84        52.44         9.63         5.03         1.02        37.05 
TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
        1.02        38.99        24.03        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-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-3666 TCGA-AA-3667 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
        2.01        14.01        47.01        15.02         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 
       19.00        36.00        85.05        37.02        33.07        36.03 
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-3952 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 
       29.98         2.01         2.01        34.03        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-A02J TCGA-AA-A02W TCGA-AA-A03J 
       37.02         2.96        39.98         5.03        41.00        40.96 
TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 
        4.21         1.58         1.02         0.20        16.31        15.75 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4681 TCGA-AZ-4684 
        0.20         5.52        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-D5-5540 TCGA-D5-5541 
       13.05        11.08        10.06        12.26        13.51        11.51 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 
       17.75         1.32         7.92        15.12        12.49        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
        7.53        10.13        12.43         9.04        13.41        11.38 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       24.43        38.20       130.65        49.91        13.32       140.38 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      131.51         6.12        26.47        35.97        60.79       117.07 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6295 
       13.38        13.64         1.55        16.31         0.53         8.35 
TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6314 
       23.51        74.56        61.87        44.68        39.42        35.93 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A50V 
       36.72        36.00        26.43        35.80        91.79         5.06 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
        5.98         5.59        17.95        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 
       19.10        12.72        37.74        10.39        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       10.39        32.02         1.02        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 
       34.03         2.01         6.05         0.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 
        0.99        29.98        32.98         0.99         1.02        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       35.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00H TCGA-AG-A00Y 
       14.04         1.02        17.03        20.98        25.97        23.01 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       15.95         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        51.98         1.94        38.96        41.00 
TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        1.45         0.72        10.19         4.73        13.97        60.03 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       10.98        11.01        12.99        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        7.10        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 
       57.24       129.27         0.49         2.40        15.85        16.34 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        11.97         8.45         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       31.30        14.86         0.39         0.66         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.46        18.28        26.43 

$`DEL PEAK 18(8P23.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
        5.06        46.65        23.38        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       16.04        14.53        32.45        30.44        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-3554 TCGA-AA-3555 TCGA-AA-3558 
       19.07        19.07        29.00        17.95        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3673 
       13.94        61.02         6.97        54.02         0.92        50.04 
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-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-3855 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 
       32.05        53.00        18.05        31.00        12.99        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        24.00        20.98         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 
       50.99        13.05        25.02        19.07        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N 
       38.04        30.02        18.05        18.05        17.03         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02         0.99        14.99        21.99        34.98 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02         0.99        32.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02H 
       35.01        35.01        26.01        39.06        51.98         2.01 
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-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-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 
        0.46         0.92        14.50        27.09         0.95        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       17.82         5.19        50.37        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
        5.13        22.36        61.41        49.41         6.77       100.01 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 
        2.24         3.06         2.14         3.25         0.26         0.33 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 
        0.10        17.56       102.44        40.34        70.16        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.01         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-5341 
       20.02        37.02         8.02        26.04         8.02        29.06 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        15.02        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       16.04        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 
       11.08        11.01        12.03        14.99        19.59        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       20.42        18.25        17.85         4.50        17.13        16.14 
TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
       12.39        14.30         9.44        11.64         1.51        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       10.26       119.70        92.75        12.59         7.50        44.32 
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-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 
       98.24        95.18         8.61        11.11        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 
       35.87        29.59        16.24        33.67         1.28        35.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 
       19.43       107.67        28.21        82.39        43.07        53.62 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       55.04        51.75        45.11        22.09        26.04        13.78 
TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV 
       26.17        46.75        47.15        52.80         4.11         2.79 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-5654 
       26.99        17.29        14.76        24.13        14.50         8.45 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 
       36.03        12.00         8.02         7.07         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 
       12.03        15.95        19.99         1.02         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4022 TCGA-AG-A008 
       36.95        13.02        14.01        48.03         0.99        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 
        6.02        37.02        36.03        49.97        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        0.49         0.69         4.60         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 
        6.97         9.37         7.99        15.02        12.00        30.05 
TCGA-DC-6681 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       12.95        24.13        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        18.28        17.69        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46        37.51         1.02         0.53         1.12 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                       140.38                        139.17 
  DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE 
                        17.03                         18.05 
[1] "0.1 - 140.4 (17.0)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.1"
D45V2, continuous
D45V3, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   179  97
  DEL PEAK 18(8P23.2) WILD-TYPE 250  62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    179   97
  DEL PEAK 18(8P23.2) WILD-TYPE  250   62
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  COLON                          179                           250
  RECTUM                          97                            62
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 18(8P23.2) MUTATED        39        0       12        64         3
  DEL PEAK 18(8P23.2) WILD-TYPE      63        1       24       101         7
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(8P23.2) MUTATED           2        14         11         40
  DEL PEAK 18(8P23.2) WILD-TYPE         1        12         11         36
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 18(8P23.2) MUTATED           32       43        12         1
  DEL PEAK 18(8P23.2) WILD-TYPE         20       17        13         0
D45V4, multiclass
            clus
vv           DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  STAGE I                             39                            63
  STAGE IA                             0                             1
  STAGE II                            12                            24
  STAGE IIA                           64                           101
  STAGE IIB                            3                             7
  STAGE IIC                            2                             1
  STAGE III                           14                            12
  STAGE IIIA                          11                            11
  STAGE IIIB                          40                            36
  STAGE IIIC                          32                            20
  STAGE IV                            43                            17
  STAGE IVA                           12                            13
  STAGE IVB                            1                             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                            T0+T1  T2  T3  T4
  DEL PEAK 18(8P23.2) MUTATED       4  47 197  30
  DEL PEAK 18(8P23.2) WILD-TYPE    16  58 206  32
D45V5, multiclass
       clus
vv      DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  T0+T1                           4                            16
  T2                             47                            58
  T3                            197                           206
  T4                             30                            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 18(8P23.2) MUTATED   130  78  68
  DEL PEAK 18(8P23.2) WILD-TYPE 205  68  40
D45V6, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  N0                         130                           205
  N1                          78                            68
  N2                          68                            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 18(8P23.2) MUTATED   195  48   5   1  26
  DEL PEAK 18(8P23.2) WILD-TYPE 248  24   4   0  32
D45V7, multiclass
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  M0                          195                           248
  M1                           48                            24
  M1A                           5                             4
  M1B                           1                             0
  MX                           26                            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"
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED   119 159
  DEL PEAK 18(8P23.2) WILD-TYPE 158 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED    119  159
  DEL PEAK 18(8P23.2) WILD-TYPE  158  156
        clus
vv       DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  FEMALE                         119                           158
  MALE                           159                           156
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                    163
  DEL PEAK 18(8P23.2) WILD-TYPE                  210
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                              15
  DEL PEAK 18(8P23.2) WILD-TYPE                            40
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                      88
  DEL PEAK 18(8P23.2) WILD-TYPE                    55
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(8P23.2) MUTATED                                7
  DEL PEAK 18(8P23.2) WILD-TYPE                              6
D45V9, multiclass
                                clus
vv                               DEL PEAK 18(8P23.2) MUTATED
  COLON ADENOCARCINOMA                                   163
  COLON MUCINOUS ADENOCARCINOMA                           15
  RECTAL ADENOCARCINOMA                                   88
  RECTAL MUCINOUS ADENOCARCINOMA                           7
                                clus
vv                               DEL PEAK 18(8P23.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     210
  COLON MUCINOUS ADENOCARCINOMA                             40
  RECTAL ADENOCARCINOMA                                     55
  RECTAL MUCINOUS ADENOCARCINOMA                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, binary
                               cls
clus                              0   1
  DEL PEAK 18(8P23.2) MUTATED     7 271
  DEL PEAK 18(8P23.2) WILD-TYPE   2 312
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(8P23.2) MUTATED      7  271
  DEL PEAK 18(8P23.2) WILD-TYPE    2  312
     clus
vv    DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  NO                            7                             2
  YES                         271                           312
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(8P23.2) MUTATED   192   2  25   8
  DEL PEAK 18(8P23.2) WILD-TYPE 234   3  11  19
D45V11, multiclass
    clus
vv   DEL PEAK 18(8P23.2) MUTATED DEL PEAK 18(8P23.2) WILD-TYPE
  R0                         192                           234
  R1                           2                             3
  R2                          25                            11
  RX                           8                            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"
D45V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(8P23.2) MUTATED                                  1     4
  DEL PEAK 18(8P23.2) WILD-TYPE                                0     8
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(8P23.2) MUTATED                          22   136
  DEL PEAK 18(8P23.2) WILD-TYPE                        22   156
D45V13, multiclass
                                  clus
vv                                 DEL PEAK 18(8P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 22
  WHITE                                                    136
                                  clus
vv                                 DEL PEAK 18(8P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        8
  BLACK OR AFRICAN AMERICAN                                   22
  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(46) Variable = DEL PEAK 19(8P22) MUTATION ANALYSIS
D46V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 19(8P22) MUTATED   220  59
  DEL PEAK 19(8P22) WILD-TYPE 237  47
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                        279                         284 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                         59                          47 
$`DEL PEAK 19(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-A00W TCGA-AA-A017 
       19.00        34.03        17.03        17.03        14.99        15.02 
TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E 
       12.00        31.00         1.02        33.04        37.02         2.96 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6899 TCGA-AD-6901 
        5.03        41.00        40.96         4.21         1.58         1.02 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
        0.20         0.46        16.31        15.75         0.20         5.52 
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-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        5.06         5.98         5.59        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 
       15.39        20.02        10.39        32.02         1.02        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 
        1.02        46.03        34.03         2.01         6.05         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 
        7.99         0.99        29.98        32.98         0.99         1.02 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       17.03        35.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y 
       36.03        14.04         1.02        17.03        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       37.02        15.95         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98         1.94        38.96 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-4957 
       41.00         1.45         0.72        10.19         4.73        13.97 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       60.03        10.98        11.01        12.99        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       36.00         7.10        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 
       41.36        57.24       129.27         0.49         2.40        15.85 
TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       16.34        11.51        10.78        13.64        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 
        9.96        31.30        14.86         0.39         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.46        18.28        26.43 

$`DEL PEAK 19(8P22) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
        5.06        46.65        23.38        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       16.04        14.53        32.45        33.53        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6653 
       32.71        22.52         8.38        24.16        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 
       20.12        19.66        16.24        24.92         1.02         3.02 
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-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
        1.02         9.07        37.05        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3534 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       19.07        29.00         0.99        17.95        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3672 TCGA-AA-3673 TCGA-AA-3675 
       13.94        61.02         6.97         0.92        50.04        47.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        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-3855 TCGA-AA-3864 TCGA-AA-3875 
       36.95        14.93        17.03        32.05        53.00        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-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3973 
        2.01        20.98         2.01        21.99        50.99        13.05 
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-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R 
       18.05        18.05         4.01        27.02        42.02         0.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I 
       21.99        34.98        15.02         0.99        32.02        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 
       38.07         1.02        35.01        35.01        26.01        39.06 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         2.01         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05         0.07        21.37        56.55         0.79         0.72 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
        0.10         0.76         0.43         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-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41        32.94         5.13        61.41        49.41         6.77 
TCGA-AZ-6601 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 
      100.01         2.24         3.06         2.14         3.25         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 
        0.33         0.10        17.56        40.34        70.16        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.01         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-5341 
       20.02        37.02         8.02        26.04         8.02        29.06 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        15.02        15.02        12.00        29.03 
TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 
       16.04        14.99        12.99        14.04        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 
       11.01        10.06        12.03        14.99        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 
       18.25        17.85         4.50        17.13        16.14        12.39 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
      119.70        92.75        12.59         7.50       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28K TCGA-DM-A28M 
      139.17        14.04        81.37       119.93        98.24        95.18 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45         6.18        35.87        29.59        16.24        33.67 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6302 
       35.41        19.43       107.67        28.21        82.39        43.07 
TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6323 
       53.62        55.04        51.75        45.11        22.09        13.78 
TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-QG-A5YV 
       26.17        47.15        52.80         4.11         2.79        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-4110 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 
       17.29        14.76        14.50         8.45        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 
        8.02         7.07         2.01        50.04        12.03        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       19.99        19.99         1.02         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       13.02        14.01        48.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
        6.02        36.03        49.97        61.97        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.69         4.60         1.81         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 
        9.37         7.99        15.02        12.00        30.05        12.95 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        17.69        16.31        16.41         8.61 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
       17.46        37.51         1.02         0.66         0.53         1.12 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                     140.38                      139.17 
  DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE 
                      17.23                       18.05 
[1] "0.1 - 140.4 (17.2)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.3"
D46V2, continuous
D46V3, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   192  98
  DEL PEAK 19(8P22) WILD-TYPE 237  61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    192   98
  DEL PEAK 19(8P22) WILD-TYPE  237   61
        clus
vv       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  COLON                        192                         237
  RECTUM                        98                          61
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 19(8P22) MUTATED        39        0       13        66         3
  DEL PEAK 19(8P22) WILD-TYPE      63        1       23        99         7
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(8P22) MUTATED           2        14         13         43
  DEL PEAK 19(8P22) WILD-TYPE         1        12          9         33
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 19(8P22) MUTATED           35       43        15         1
  DEL PEAK 19(8P22) WILD-TYPE         17       17        10         0
D46V4, multiclass
            clus
vv           DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  STAGE I                           39                          63
  STAGE IA                           0                           1
  STAGE II                          13                          23
  STAGE IIA                         66                          99
  STAGE IIB                          3                           7
  STAGE IIC                          2                           1
  STAGE III                         14                          12
  STAGE IIIA                        13                           9
  STAGE IIIB                        43                          33
  STAGE IIIC                        35                          17
  STAGE IV                          43                          17
  STAGE IVA                         15                          10
  STAGE IVB                          1                           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                          T0+T1  T2  T3  T4
  DEL PEAK 19(8P22) MUTATED       5  46 208  33
  DEL PEAK 19(8P22) WILD-TYPE    15  59 195  29
D46V5, multiclass
       clus
vv      DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  T0+T1                         5                          15
  T2                           46                          59
  T3                          208                         195
  T4                           33                          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
  DEL PEAK 19(8P22) MUTATED   134  82  74
  DEL PEAK 19(8P22) WILD-TYPE 201  64  34
D46V6, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  N0                       134                         201
  N1                        82                          64
  N2                        74                          34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A M1B  MX
  DEL PEAK 19(8P22) MUTATED   205  51   5   1  27
  DEL PEAK 19(8P22) WILD-TYPE 238  21   4   0  31
D46V7, multiclass
     clus
vv    DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  M0                        205                         238
  M1                         51                          21
  M1A                         5                           4
  M1B                         1                           0
  MX                         27                          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"
D46V8, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED   128 164
  DEL PEAK 19(8P22) WILD-TYPE 149 151
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED    128  164
  DEL PEAK 19(8P22) WILD-TYPE  149  151
        clus
vv       DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  FEMALE                       128                         149
  MALE                         164                         151
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                    175
  DEL PEAK 19(8P22) WILD-TYPE                  198
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                              16
  DEL PEAK 19(8P22) WILD-TYPE                            39
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                      89
  DEL PEAK 19(8P22) WILD-TYPE                    54
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(8P22) MUTATED                                7
  DEL PEAK 19(8P22) WILD-TYPE                              6
D46V9, multiclass
                                clus
vv                               DEL PEAK 19(8P22) MUTATED
  COLON ADENOCARCINOMA                                 175
  COLON MUCINOUS ADENOCARCINOMA                         16
  RECTAL ADENOCARCINOMA                                 89
  RECTAL MUCINOUS ADENOCARCINOMA                         7
                                clus
vv                               DEL PEAK 19(8P22) WILD-TYPE
  COLON ADENOCARCINOMA                                   198
  COLON MUCINOUS ADENOCARCINOMA                           39
  RECTAL ADENOCARCINOMA                                   54
  RECTAL MUCINOUS ADENOCARCINOMA                           6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, binary
                             cls
clus                            0   1
  DEL PEAK 19(8P22) MUTATED     8 284
  DEL PEAK 19(8P22) WILD-TYPE   1 299
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 19(8P22) MUTATED      8  284
  DEL PEAK 19(8P22) WILD-TYPE    1  299
     clus
vv    DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  NO                          8                           1
  YES                       284                         299
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 19(8P22) MUTATED   205   2  25   8
  DEL PEAK 19(8P22) WILD-TYPE 221   3  11  19
D46V11, multiclass
    clus
vv   DEL PEAK 19(8P22) MUTATED DEL PEAK 19(8P22) WILD-TYPE
  R0                       205                         221
  R1                         2                           3
  R2                        25                          11
  RX                         8                          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"
D46V12, continuous
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(8P22) MUTATED                                  1     4
  DEL PEAK 19(8P22) WILD-TYPE                                0     8
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(8P22) MUTATED                          22   147
  DEL PEAK 19(8P22) WILD-TYPE                        22   145
D46V13, multiclass
                                  clus
vv                                 DEL PEAK 19(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                               22
  WHITE                                                  147
                                  clus
vv                                 DEL PEAK 19(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      8
  BLACK OR AFRICAN AMERICAN                                 22
  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(47) Variable = DEL PEAK 20(8P11.21) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(8P11.21) MUTATED    95  28
  DEL PEAK 20(8P11.21) WILD-TYPE 362  78
  DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE 
                           123                            440 
  DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE 
                            28                             78 
$`DEL PEAK 20(8P11.21) MUTATED`
TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3810 
       43.76        42.28        44.91        35.11        15.52        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A567 
       32.91        31.63        25.08        20.61        23.87        61.84 
TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3496 TCGA-AA-3517 TCGA-AA-3520 
       52.44         5.03         1.02         1.02        38.99        24.03 
TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       34.03        29.00        14.01        21.01        13.02        24.00 
TCGA-AA-3560 TCGA-AA-3666 TCGA-AA-3692 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3860 
       19.99         2.01        36.00        37.02        33.07        31.07 
TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3956 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00D 
       17.03         2.01        34.03        26.01         7.96        19.00 
TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       17.03         0.99        12.00        31.00         1.02        33.04 
TCGA-AA-A02E TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 
        2.96         1.02         0.20         0.20         5.52        75.25 
TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
       65.00        12.10        29.56         5.23        11.74         1.94 
TCGA-CM-4751 TCGA-CM-5868 TCGA-CM-6675 TCGA-CM-6676 TCGA-D5-5538 TCGA-D5-5540 
       27.02        17.03        13.05        11.08        12.26        13.51 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6929 TCGA-DM-A1D6 
       17.75         7.92        15.12        12.49        13.41        49.91 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6460 
      140.38       131.51        26.47        35.97        60.79        13.38 
TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6303 
       13.64         1.55        16.31        23.51        74.56        61.87 
TCGA-G4-6306 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6625 TCGA-AF-2689 TCGA-AF-2690 
       44.68        35.93        36.00        91.79        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3578 TCGA-AG-3586 TCGA-AG-3587 
       43.04        13.55        12.72        32.02         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3883 
       34.03         7.99         0.99        29.98         0.99         1.02 
TCGA-AG-3890 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        28.04        14.04        17.03        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 
       37.02         1.02        12.00        70.03        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6547 TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-5869 
        1.94        38.96         1.45        10.19         4.73        12.99 
TCGA-DC-6155 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6885 TCGA-EI-7002 
       13.97       126.44       129.27        51.48        13.64        11.97 
TCGA-F5-6810 TCGA-F5-6863 TCGA-G5-6641 
        0.39         0.76        26.43 

$`DEL PEAK 20(8P11.21) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        37.02        46.65        43.43        23.38        17.79 
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       45.60        13.94        37.05        37.25        16.04        34.65 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       14.53        32.45        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-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.18        24.16        21.76        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-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3506 
        9.63         1.02         3.02        37.05        35.01        58.03 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        13.02         1.02         9.07 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3534 
       37.05        36.03         8.05        19.07        19.07        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3554 TCGA-AA-3555 
       26.01        12.99         0.99        33.99        17.95        29.95 
TCGA-AA-3556 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        20.98        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3673 
        6.05         6.97        54.02        14.01         0.92        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 
       47.05        47.01        15.02        11.01         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 
       19.00         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-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3867 
       36.03        32.05         0.99        31.07        53.00        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-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        20.98         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-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-A00W TCGA-AA-A00Z TCGA-AA-A010 
       27.02        42.02         0.99        14.99        21.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        15.02        32.02        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-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-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-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-4313 
        0.95        15.75        21.44        17.82         5.19        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-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 
       22.36        62.79        61.41        49.41         6.77       100.01 
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-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        21.01         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-4752 
       20.02        37.02         8.02        26.04         8.02        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-6677 TCGA-CM-6678 
       15.02        14.04        11.01        12.95        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       10.06        12.03        14.99        19.59        11.51        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       20.42        18.25         1.32        17.85         4.50        17.13 
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-D5-6932 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-A1DA TCGA-DM-A1DB TCGA-DM-A1HB 
       92.75        13.32        12.59         7.50        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17         6.12        14.04        81.37       119.93 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 
      117.07        98.24        95.18         8.61        11.11        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        6.18        35.87        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-G4-6302 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-G4-6311 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-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       35.80        26.17        46.75        47.15        52.80         4.11 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        5.06         2.79         5.98         5.59        26.99        17.29 
TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       14.76        24.13        19.10        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
        8.45        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3594 
        8.02         7.07         1.02         2.01        24.00         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       19.99         1.02        32.98         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       19.99        36.03         1.02         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01Y 
        6.02        15.95        36.03         9.07        31.00        64.01 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       49.97        61.97        41.00        38.04         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.00        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.31        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        8.45         9.96        37.51        31.30        14.86         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE 
                         17.95                          17.90 
[1] "0.2 - 140.4 (17.9)" "0.1 - 139.2 (17.9)"
[1] "hr=" "1.2"
D47V2, continuous
D47V3, binary
                                cls
clus                               0   1
  DEL PEAK 20(8P11.21) MUTATED    83  44
  DEL PEAK 20(8P11.21) WILD-TYPE 346 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(8P11.21) MUTATED     83   44
  DEL PEAK 20(8P11.21) WILD-TYPE  346  115
        clus
vv       DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE
  COLON                            83                            346
  RECTUM                           44                            115
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 20(8P11.21) MUTATED        14        0        5        33         1
  DEL PEAK 20(8P11.21) WILD-TYPE      88        1       31       132         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8P11.21) MUTATED           0         7          6         19
  DEL PEAK 20(8P11.21) WILD-TYPE         3        19         16         57
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 20(8P11.21) MUTATED           13       21         4         1
  DEL PEAK 20(8P11.21) WILD-TYPE         39       39        21         0
D47V4, multiclass
            clus
vv           DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE
  STAGE I                              14                             88
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            33                            132
  STAGE IIB                             1                              9
  STAGE IIC                             0                              3
  STAGE III                             7                             19
  STAGE IIIA                            6                             16
  STAGE IIIB                           19                             57
  STAGE IIIC                           13                             39
  STAGE IV                             21                             39
  STAGE IVA                             4                             21
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 20(8P11.21) MUTATED       3  19  96  10
  DEL PEAK 20(8P11.21) WILD-TYPE    17  86 307  52
D47V5, multiclass
       clus
vv      DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE
  T0+T1                            3                             17
  T2                              19                             86
  T3                              96                            307
  T4                              10                             52
[1] 4 2
[1] TRUE
[1] "dimension 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(8P11.21) MUTATED    58  41  29
  DEL PEAK 20(8P11.21) WILD-TYPE 277 105  79
D47V6, multiclass
    clus
vv   DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE
  N0                           58                            277
  N1                           41                            105
  N2                           29                             79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 20(8P11.21) MUTATED    89  23   2   1  10
  DEL PEAK 20(8P11.21) WILD-TYPE 354  49   7   0  48
D47V7, multiclass
     clus
vv    DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE
  M0                            89                            354
  M1                            23                             49
  M1A                            2                              7
  M1B                            1                              0
  MX                            10                             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"
D47V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(8P11.21) MUTATED    63  65
  DEL PEAK 20(8P11.21) WILD-TYPE 214 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(8P11.21) MUTATED     63   65
  DEL PEAK 20(8P11.21) WILD-TYPE  214  250
        clus
vv       DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE
  FEMALE                           63                            214
  MALE                             65                            250
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 20(8P11.21) MUTATED                     74
  DEL PEAK 20(8P11.21) WILD-TYPE                  299
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(8P11.21) MUTATED                               9
  DEL PEAK 20(8P11.21) WILD-TYPE                            46
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 20(8P11.21) MUTATED                      39
  DEL PEAK 20(8P11.21) WILD-TYPE                   104
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(8P11.21) MUTATED                                4
  DEL PEAK 20(8P11.21) WILD-TYPE                              9
D47V9, multiclass
                                clus
vv                               DEL PEAK 20(8P11.21) MUTATED
  COLON ADENOCARCINOMA                                     74
  COLON MUCINOUS ADENOCARCINOMA                             9
  RECTAL ADENOCARCINOMA                                    39
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               DEL PEAK 20(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      299
  COLON MUCINOUS ADENOCARCINOMA                              46
  RECTAL ADENOCARCINOMA                                     104
  RECTAL MUCINOUS ADENOCARCINOMA                              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"
D47V10, binary
                                cls
clus                               0   1
  DEL PEAK 20(8P11.21) MUTATED     3 125
  DEL PEAK 20(8P11.21) WILD-TYPE   6 458
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(8P11.21) MUTATED      3  125
  DEL PEAK 20(8P11.21) WILD-TYPE    6  458
     clus
vv    DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE
  NO                             3                              6
  YES                          125                            458
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 20(8P11.21) MUTATED    92   1   9   1
  DEL PEAK 20(8P11.21) WILD-TYPE 334   4  27  26
D47V11, multiclass
    clus
vv   DEL PEAK 20(8P11.21) MUTATED DEL PEAK 20(8P11.21) WILD-TYPE
  R0                           92                            334
  R1                            1                              4
  R2                            9                             27
  RX                            1                             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"
D47V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(8P11.21) MUTATED                                  1     0
  DEL PEAK 20(8P11.21) WILD-TYPE                                0    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(8P11.21) MUTATED                          10    60
  DEL PEAK 20(8P11.21) WILD-TYPE                        34   232
D47V13, multiclass
                                  clus
vv                                 DEL PEAK 20(8P11.21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      60
                                  clus
vv                                 DEL PEAK 20(8P11.21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    34
  WHITE                                                       232
[1] 4 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 21(8Q11.1) MUTATION ANALYSIS
D48V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(8Q11.1) MUTATED    34  11
  DEL PEAK 21(8Q11.1) WILD-TYPE 423  95
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           45                           518 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           11                            95 
$`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-CM-4746 TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-5540 TCGA-D5-6531 
        5.52        37.02        17.03        13.05        13.51        17.75 
TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-F4-6704 TCGA-G4-6298 TCGA-G4-6625 TCGA-AF-2689 
       49.91       131.51         1.55        23.51        91.79        17.95 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3582 TCGA-AG-3728 TCGA-AG-3890 TCGA-AG-3909 
       13.55        12.72         1.02        29.98        17.03        19.99 
TCGA-AG-A01L TCGA-AG-A02G TCGA-AG-A02X TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DG 
       12.00        38.96        41.00        13.97        15.02        51.48 
TCGA-EI-6513 TCGA-F5-6810 TCGA-F5-6813 
       16.34         0.39         0.69 

$`DEL PEAK 21(8Q11.1) 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-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       35.11        45.60        13.94        37.05        37.25        16.04 
TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       34.65        14.53        32.45        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-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.18        24.16        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-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-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 
       13.02         1.02         9.07        24.03        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        8.05        19.07        19.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3553 
       12.99         0.99        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-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-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01        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-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        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-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-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-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        17.03         4.01        27.02        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-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
       35.01         1.02        33.04        35.01        26.01        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-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-6899 
       21.37         4.21        56.55         0.79         0.72         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-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        15.75 
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-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-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        2.24         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-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 
       21.01         2.93         2.01       124.27        23.05        20.02 
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-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 
       15.02        15.02        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-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 
       10.06        12.03        14.99        12.26        19.59        11.51 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
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-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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-A1HB 
       13.32        12.59       140.38         7.50        44.32       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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        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-G4-6295 
        0.53        35.41        19.43       107.67        28.21         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        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-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       26.17        46.75        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50         8.45        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        61.97        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
       10.98        11.01        15.02        12.99        12.00        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        7.10        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
        9.96        37.51        31.30        14.86         1.02         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  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 
                       17.750                        18.015 
[1] "0.2 - 131.5 (17.8)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.3"
D48V2, continuous
D48V3, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    29  16
  DEL PEAK 21(8Q11.1) WILD-TYPE 400 143
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     29   16
  DEL PEAK 21(8Q11.1) WILD-TYPE  400  143
        clus
vv       DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  COLON                           29                           400
  RECTUM                          16                           143
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 21(8Q11.1) MUTATED         4        0        0        13         1
  DEL PEAK 21(8Q11.1) WILD-TYPE      98        1       36       152         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 21(8Q11.1) MUTATED           0         2          2          7
  DEL PEAK 21(8Q11.1) WILD-TYPE         3        24         20         69
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 21(8Q11.1) MUTATED            7        6         3         1
  DEL PEAK 21(8Q11.1) WILD-TYPE         45       54        22         0
D48V4, multiclass
            clus
vv           DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  STAGE I                              4                            98
  STAGE IA                             0                             1
  STAGE II                             0                            36
  STAGE IIA                           13                           152
  STAGE IIB                            1                             9
  STAGE IIC                            0                             3
  STAGE III                            2                            24
  STAGE IIIA                           2                            20
  STAGE IIIB                           7                            69
  STAGE IIIC                           7                            45
  STAGE IV                             6                            54
  STAGE IVA                            3                            22
  STAGE IVB                            1                             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                            T0+T1  T2  T3  T4
  DEL PEAK 21(8Q11.1) MUTATED       0   7  34   5
  DEL PEAK 21(8Q11.1) WILD-TYPE    20  98 369  57
D48V5, multiclass
       clus
vv      DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  T0+T1                           0                            20
  T2                              7                            98
  T3                             34                           369
  T4                              5                            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"
                               vv
clus                             N0  N1  N2
  DEL PEAK 21(8Q11.1) MUTATED    19  16  11
  DEL PEAK 21(8Q11.1) WILD-TYPE 316 130  97
D48V6, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  N0                          19                           316
  N1                          16                           130
  N2                          11                            97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 21(8Q11.1) MUTATED    32   7   2   1   2
  DEL PEAK 21(8Q11.1) WILD-TYPE 411  65   7   0  56
D48V7, multiclass
     clus
vv    DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  M0                           32                           411
  M1                            7                            65
  M1A                           2                             7
  M1B                           1                             0
  MX                            2                            56
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    18  28
  DEL PEAK 21(8Q11.1) WILD-TYPE 259 287
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     18   28
  DEL PEAK 21(8Q11.1) WILD-TYPE  259  287
        clus
vv       DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  FEMALE                          18                           259
  MALE                            28                           287
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 21(8Q11.1) MUTATED                     25
  DEL PEAK 21(8Q11.1) WILD-TYPE                  348
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(8Q11.1) MUTATED                               4
  DEL PEAK 21(8Q11.1) WILD-TYPE                            51
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 21(8Q11.1) MUTATED                      15
  DEL PEAK 21(8Q11.1) WILD-TYPE                   128
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(8Q11.1) MUTATED                                1
  DEL PEAK 21(8Q11.1) WILD-TYPE                             12
D48V9, multiclass
                                clus
vv                               DEL PEAK 21(8Q11.1) MUTATED
  COLON ADENOCARCINOMA                                    25
  COLON MUCINOUS ADENOCARCINOMA                            4
  RECTAL ADENOCARCINOMA                                   15
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 21(8Q11.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     348
  COLON MUCINOUS ADENOCARCINOMA                             51
  RECTAL ADENOCARCINOMA                                    128
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D48V10, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED     1  45
  DEL PEAK 21(8Q11.1) WILD-TYPE   8 538
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED      1   45
  DEL PEAK 21(8Q11.1) WILD-TYPE    8  538
     clus
vv    DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  NO                            1                             8
  YES                          45                           538
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(8Q11.1) MUTATED    37   0   4   0
  DEL PEAK 21(8Q11.1) WILD-TYPE 389   5  32  27
D48V11, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  R0                          37                           389
  R1                           0                             5
  R2                           4                            32
  RX                           0                            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"
D48V12, 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    12
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(8Q11.1) MUTATED                           5    22
  DEL PEAK 21(8Q11.1) WILD-TYPE                        39   270
D48V13, multiclass
                                  clus
vv                                 DEL PEAK 21(8Q11.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     22
                                  clus
vv                                 DEL PEAK 21(8Q11.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                       12
  BLACK OR AFRICAN AMERICAN                                   39
  WHITE                                                      270
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = DEL PEAK 22(9P24.2) MUTATION ANALYSIS
D49V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(9P24.2) MUTATED    61  16
  DEL PEAK 22(9P24.2) WILD-TYPE 396  90
  DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE 
                           77                           486 
  DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE 
                           16                            90 
$`DEL PEAK 22(9P24.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5667 TCGA-A6-6649 
       37.02        43.43        36.53        14.53        29.16        24.16 
TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 
       21.76        61.84         6.97        38.99         9.07        29.00 
TCGA-AA-3553 TCGA-AA-3562 TCGA-AA-3685 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3867 
       24.00        19.99        37.05        85.05        25.02        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-A03J TCGA-AD-6888 TCGA-AD-6965 TCGA-AY-4070 TCGA-AZ-4614 TCGA-AZ-6605 
       40.96         4.21         0.20        16.31         5.65         5.23 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 TCGA-CM-5348 
        3.19         1.94         3.29         0.26         8.02        22.98 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       13.02        15.02        13.05        11.08        11.01        10.06 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6898 TCGA-DM-A0XF TCGA-DM-A288 
       20.19         1.32         7.92         7.53        38.20        14.04 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-NH-A6GA TCGA-AF-2687 TCGA-AF-2692 
       33.67         8.35        82.39         5.98        24.13        13.55 
TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3896 
        2.01        34.03         6.05         1.02        19.99         1.02 
TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6544 TCGA-BM-6198 
       15.95        12.00         1.94        38.96         0.49        10.19 
TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-6160 TCGA-DY-A1DD 
        6.05         4.73        13.97        11.01        30.05        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6514 TCGA-F5-6814 
       24.13        51.48         0.49        16.31         0.53 

$`DEL PEAK 22(9P24.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.76        23.38        17.79        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        16.04        34.65        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-A6-6137 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-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        20.61        24.69        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        20.28        16.24        24.92        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-3514 TCGA-AA-3516 TCGA-AA-3518 
       35.01        58.03        63.98         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-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 
       34.03        29.00        26.01        12.99         0.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        13.02        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-3673 
        6.97        54.02         2.01        14.01         0.92        50.04 
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-3692 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 
       36.00         5.03        26.99        19.04         0.99         0.99 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       35.05         0.99         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-3851 
       36.95        37.02        14.93        17.03         0.99        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-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-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        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-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-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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98        15.02        15.02         0.99        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-6889 
       41.00        39.98        18.05         0.07        21.37        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-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.43         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-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-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-6600 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5254 
        6.77        12.10       100.01        29.56        11.74         2.24 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         2.14         3.25         0.07         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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       48.20        51.32        21.99        21.01         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-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        29.06        22.03        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-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6680 
       12.99        14.04        11.01        12.95        11.08        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       14.99        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25        15.12        17.85         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-A1D0 
       12.00        11.38        10.26       119.70        24.43       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-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-F4-6461 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-F4-6809 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-G4-6310 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-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        4.11         5.06         2.79         5.59        26.99        17.29 
TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       14.76        17.95        17.23        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
        1.02        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99        29.98        32.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       23.01        37.02        36.03         9.07         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       70.03        64.01        10.98        51.98        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        1.81         6.05         6.97         9.37        60.03         7.99 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       10.98        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       36.00         7.10        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
      126.44        41.36       129.27        32.61         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       14.86         0.39         1.02         0.66         0.69         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE 
                         0.20                          0.07 
  DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE 
                        85.05                        140.38 
  DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE 
                        14.04                         18.05 
[1] "0.2 - 85.0 (14.0)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.4"
D49V2, continuous
D49V3, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P24.2) MUTATED    55  25
  DEL PEAK 22(9P24.2) WILD-TYPE 374 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P24.2) MUTATED     55   25
  DEL PEAK 22(9P24.2) WILD-TYPE  374  134
        clus
vv       DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE
  COLON                           55                           374
  RECTUM                          25                           134
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 22(9P24.2) MUTATED        13        0        4        18         1
  DEL PEAK 22(9P24.2) WILD-TYPE      89        1       32       147         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(9P24.2) MUTATED           0         3          3         12
  DEL PEAK 22(9P24.2) WILD-TYPE         3        23         19         64
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 22(9P24.2) MUTATED            8       12         4         1
  DEL PEAK 22(9P24.2) WILD-TYPE         44       48        21         0
D49V4, multiclass
            clus
vv           DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE
  STAGE I                             13                            89
  STAGE IA                             0                             1
  STAGE II                             4                            32
  STAGE IIA                           18                           147
  STAGE IIB                            1                             9
  STAGE IIC                            0                             3
  STAGE III                            3                            23
  STAGE IIIA                           3                            19
  STAGE IIIB                          12                            64
  STAGE IIIC                           8                            44
  STAGE IV                            12                            48
  STAGE IVA                            4                            21
  STAGE IVB                            1                             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                            T0+T1  T2  T3  T4
  DEL PEAK 22(9P24.2) MUTATED       2  17  50  12
  DEL PEAK 22(9P24.2) WILD-TYPE    18  88 353  50
D49V5, multiclass
       clus
vv      DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE
  T0+T1                           2                            18
  T2                             17                            88
  T3                             50                           353
  T4                             12                            50
[1] 4 2
[1] TRUE
[1] "dimension 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(9P24.2) MUTATED    38  23  19
  DEL PEAK 22(9P24.2) WILD-TYPE 297 123  89
D49V6, multiclass
    clus
vv   DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE
  N0                          38                           297
  N1                          23                           123
  N2                          19                            89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A M1B  MX
  DEL PEAK 22(9P24.2) MUTATED    56  15   2   1   6
  DEL PEAK 22(9P24.2) WILD-TYPE 387  57   7   0  52
D49V7, multiclass
     clus
vv    DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE
  M0                           56                           387
  M1                           15                            57
  M1A                           2                             7
  M1B                           1                             0
  MX                            6                            52
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V8, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P24.2) MUTATED    29  52
  DEL PEAK 22(9P24.2) WILD-TYPE 248 263
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P24.2) MUTATED     29   52
  DEL PEAK 22(9P24.2) WILD-TYPE  248  263
        clus
vv       DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE
  FEMALE                          29                           248
  MALE                            52                           263
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 22(9P24.2) MUTATED                     52
  DEL PEAK 22(9P24.2) WILD-TYPE                  321
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(9P24.2) MUTATED                               3
  DEL PEAK 22(9P24.2) WILD-TYPE                            52
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 22(9P24.2) MUTATED                      24
  DEL PEAK 22(9P24.2) WILD-TYPE                   119
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(9P24.2) MUTATED                                1
  DEL PEAK 22(9P24.2) WILD-TYPE                             12
D49V9, multiclass
                                clus
vv                               DEL PEAK 22(9P24.2) MUTATED
  COLON ADENOCARCINOMA                                    52
  COLON MUCINOUS ADENOCARCINOMA                            3
  RECTAL ADENOCARCINOMA                                   24
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 22(9P24.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     321
  COLON MUCINOUS ADENOCARCINOMA                             52
  RECTAL ADENOCARCINOMA                                    119
  RECTAL MUCINOUS ADENOCARCINOMA                            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"
D49V10, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P24.2) MUTATED     2  79
  DEL PEAK 22(9P24.2) WILD-TYPE   7 504
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P24.2) MUTATED      2   79
  DEL PEAK 22(9P24.2) WILD-TYPE    7  504
     clus
vv    DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE
  NO                            2                             7
  YES                          79                           504
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(9P24.2) MUTATED    52   2   7   2
  DEL PEAK 22(9P24.2) WILD-TYPE 374   3  29  25
D49V11, multiclass
    clus
vv   DEL PEAK 22(9P24.2) MUTATED DEL PEAK 22(9P24.2) WILD-TYPE
  R0                          52                           374
  R1                           2                             3
  R2                           7                            29
  RX                           2                            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"
D49V12, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(9P24.2) MUTATED                                  0     2
  DEL PEAK 22(9P24.2) WILD-TYPE                                1    10
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(9P24.2) MUTATED                           5    43
  DEL PEAK 22(9P24.2) WILD-TYPE                        39   249
D49V13, multiclass
                                  clus
vv                                 DEL PEAK 22(9P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     43
                                  clus
vv                                 DEL PEAK 22(9P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                       10
  BLACK OR AFRICAN AMERICAN                                   39
  WHITE                                                      249
[1] 4 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 23(10Q21.1) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(10Q21.1) MUTATED    97  24
  DEL PEAK 23(10Q21.1) WILD-TYPE 360  82
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                           121                            442 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                            24                             82 
$`DEL PEAK 23(10Q21.1) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-4107 TCGA-A6-5659 
       37.02        17.79        35.11        45.60        32.45        30.44 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 
       32.71        29.16        22.52        25.18        20.61        23.87 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3517 
       61.84        52.44         9.63         1.02         6.97        38.99 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3673 TCGA-AA-3685 
       33.99        13.02        19.99         6.05        50.04        37.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 
       36.00        85.05         0.99        31.07        17.03        24.03 
TCGA-AA-3952 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q 
        2.01        21.99        50.99         7.96        34.03        42.02 
TCGA-AA-A01D TCGA-AA-A01Q TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02W 
        0.99         1.02        26.01        39.98         5.03        41.00 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4614 
        1.02         0.43        14.50        16.31         0.20         5.65 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5797 
       65.00        62.79        29.56         3.19         2.24         3.29 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
        0.26         1.35         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-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6898 
       11.08        17.75         7.92        15.12        17.85         7.53 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DB 
        9.04        13.41        12.00        11.38        12.59        44.32 
TCGA-DM-A28H TCGA-F4-6461 TCGA-G4-6307 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6322 
      117.07        11.11        55.04        35.93        36.72        26.04 
TCGA-G4-6625 TCGA-G4-6626 TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 
       91.79        46.75        24.13        13.55        12.72        10.39 
TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3883 
       32.02        46.03        34.03         6.05        29.98         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.95         1.02        19.99        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02X TCGA-CI-6622 TCGA-CI-6624 
       23.01        12.00         1.94        41.00         6.97         4.73 
TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       13.97        13.97        36.00         7.10        13.05        10.06 
TCGA-DY-A1DE TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6864 
      129.27        17.00        16.31        16.41        14.86         0.46 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 23(10Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
        5.06        46.65        43.76        43.43        23.38        42.28 
TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        13.94        15.52        37.05        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       34.65        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-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-3663 TCGA-AA-3664 
       19.99        13.94        61.02        78.08         6.97        54.02 
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-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 
       34.03         2.01        16.08        13.05        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-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V 
       31.00        38.07        35.01         1.02        33.04        35.01 
TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O 
       37.02        39.06        51.98         2.96         2.01         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-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
        0.76         0.20         0.46         0.92        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-4615 TCGA-AZ-4616 TCGA-AZ-4681 
       50.37        58.39         1.41        32.94         5.13        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-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74         1.94         3.06         2.14         3.25 
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-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       70.16        15.62        48.20        51.32        21.99        21.01 
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-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
        8.02        26.04        27.02        13.02        22.98        30.08 
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-6675 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        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-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       18.25         1.32         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       15.58        12.39        10.13        12.43        14.30         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-A1D9 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32       140.38         7.50 
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-A28K 
       26.47        81.37       119.93        35.97        60.79        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        13.38        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-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6317 
       53.62        44.68        51.75        45.11        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 
       26.43        22.09        13.78        35.80        26.17        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       52.80         4.11         5.06         2.79         5.98         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       26.99        17.29        14.76        17.95        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       20.02        36.03        12.00         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        2.01        24.00         1.02         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 
        1.02        32.98         0.99         0.99        19.99        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 
       13.02        35.01        14.01        48.03        32.02        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 
        4.60         1.81        10.19         6.05         6.05         9.37 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       12.00        15.02        30.05        12.95         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.76        18.28        55.76        47.08 

  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                        129.27                         140.38 
  DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE 
                         17.00                          18.05 
[1] "0.2 - 129.3 (17.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.1"
D50V2, continuous
D50V3, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    89  36
  DEL PEAK 23(10Q21.1) WILD-TYPE 340 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     89   36
  DEL PEAK 23(10Q21.1) WILD-TYPE  340  123
        clus
vv       DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  COLON                            89                            340
  RECTUM                           36                            123
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 23(10Q21.1) MUTATED        19        0        7        31         1
  DEL PEAK 23(10Q21.1) WILD-TYPE      83        1       29       134         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(10Q21.1) MUTATED           1         2          7         16
  DEL PEAK 23(10Q21.1) WILD-TYPE         2        24         15         60
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 23(10Q21.1) MUTATED           17       17         5         0
  DEL PEAK 23(10Q21.1) WILD-TYPE         35       43        20         1
D50V4, multiclass
            clus
vv           DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  STAGE I                              19                             83
  STAGE IA                              0                              1
  STAGE II                              7                             29
  STAGE IIA                            31                            134
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                             2                             24
  STAGE IIIA                            7                             15
  STAGE IIIB                           16                             60
  STAGE IIIC                           17                             35
  STAGE IV                             17                             43
  STAGE IVA                             5                             20
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 23(10Q21.1) MUTATED       2  23  88  13
  DEL PEAK 23(10Q21.1) WILD-TYPE    18  82 315  49
D50V5, multiclass
       clus
vv      DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  T0+T1                            2                             18
  T2                              23                             82
  T3                              88                            315
  T4                              13                             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 23(10Q21.1) MUTATED    64  34  28
  DEL PEAK 23(10Q21.1) WILD-TYPE 271 112  80
D50V6, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  N0                           64                            271
  N1                           34                            112
  N2                           28                             80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 23(10Q21.1) MUTATED    94  19   2   0   9
  DEL PEAK 23(10Q21.1) WILD-TYPE 349  53   7   1  49
D50V7, multiclass
     clus
vv    DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  M0                            94                            349
  M1                            19                             53
  M1A                            2                              7
  M1B                            0                              1
  MX                             9                             49
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED    59  67
  DEL PEAK 23(10Q21.1) WILD-TYPE 218 248
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED     59   67
  DEL PEAK 23(10Q21.1) WILD-TYPE  218  248
        clus
vv       DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  FEMALE                           59                            218
  MALE                             67                            248
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                     83
  DEL PEAK 23(10Q21.1) WILD-TYPE                  290
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                               6
  DEL PEAK 23(10Q21.1) WILD-TYPE                            49
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                      31
  DEL PEAK 23(10Q21.1) WILD-TYPE                   112
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(10Q21.1) MUTATED                                5
  DEL PEAK 23(10Q21.1) WILD-TYPE                              8
D50V9, multiclass
                                clus
vv                               DEL PEAK 23(10Q21.1) MUTATED
  COLON ADENOCARCINOMA                                     83
  COLON MUCINOUS ADENOCARCINOMA                             6
  RECTAL ADENOCARCINOMA                                    31
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 23(10Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      290
  COLON MUCINOUS ADENOCARCINOMA                              49
  RECTAL ADENOCARCINOMA                                     112
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, binary
                                cls
clus                               0   1
  DEL PEAK 23(10Q21.1) MUTATED     5 121
  DEL PEAK 23(10Q21.1) WILD-TYPE   4 462
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10Q21.1) MUTATED      5  121
  DEL PEAK 23(10Q21.1) WILD-TYPE    4  462
     clus
vv    DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  NO                             5                              4
  YES                          121                            462
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(10Q21.1) MUTATED    89   2  10   6
  DEL PEAK 23(10Q21.1) WILD-TYPE 337   3  26  21
D50V11, multiclass
    clus
vv   DEL PEAK 23(10Q21.1) MUTATED DEL PEAK 23(10Q21.1) WILD-TYPE
  R0                           89                            337
  R1                            2                              3
  R2                           10                             26
  RX                            6                             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"
D50V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(10Q21.1) MUTATED                                  0     4
  DEL PEAK 23(10Q21.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(10Q21.1) MUTATED                           9    64
  DEL PEAK 23(10Q21.1) WILD-TYPE                        35   228
D50V13, multiclass
                                  clus
vv                                 DEL PEAK 23(10Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      64
                                  clus
vv                                 DEL PEAK 23(10Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       228
[1] 4 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 24(10Q23.31) MUTATION ANALYSIS
D51V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 24(10Q23.31) MUTATED   121  24
  DEL PEAK 24(10Q23.31) WILD-TYPE 336  82
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                            145                             418 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                             24                              82 
$`DEL PEAK 24(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-AF-2687 TCGA-AF-2689 
       36.00        26.04        13.78        46.75        24.13        17.95 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3586 TCGA-AG-3587 
       13.55        12.72        10.39        32.02         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3887 
       34.03        50.04         6.05        29.98         1.02        36.95 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L 
        1.02        19.99        13.94        25.97        37.02        12.00 
TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6624 
       10.98        41.00         4.60        10.19         6.97         4.73 
TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
       13.97        13.97        36.00        13.05        10.06       129.27 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 
       24.13         0.49         2.40        17.00        16.34        16.31 
TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 
       16.41        11.97        14.86         0.66         0.46        47.08 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 24(10Q23.31) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 
        5.06        46.65        43.76        43.43        23.38        44.91 
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-A6-5656 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-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        24.13         8.38        25.08 
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-A56B TCGA-AA-3488 TCGA-AA-3489 
       20.28        16.24        24.92        52.44         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-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3522 
        1.02        13.02        38.99         1.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3534 
       36.03         8.05        19.07        34.03        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99         0.99        14.01        21.01        24.00 
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-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.97         2.01        14.01         0.92        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02         5.98        19.00         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-3842 TCGA-AA-3844 
        1.02        17.98        15.95        38.99        37.02        14.93 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
       17.03         0.99        36.03        32.05         0.99        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-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-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        32.02        12.00        31.00 
TCGA-AA-A01K 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-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-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-4071 
        0.10         0.76         0.20         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4313 
       15.75         0.20        21.44        17.82        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-6605 
       61.41        49.41         6.77        12.10       100.01         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         1.94         3.06         2.14         3.25         0.07 
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-4952 TCGA-CK-5912 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       15.62        48.20        51.32        21.99        21.01         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-4752 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       26.04        27.02        13.02        22.98        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-6678 
       14.99        12.99        14.04        11.01        12.95        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-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 
       20.42         1.32        15.12         4.50        17.13        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-D5-6932 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-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB 
       38.20        92.75        49.91        12.59         7.50        44.32 
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-A28K 
       81.37       119.93        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        13.38        13.64        13.45         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 
       35.87         1.55        16.31        29.59         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-G4-6298 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-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       51.75        45.11        39.42        35.93        26.43        22.09 
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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        5.06         2.79         5.98         5.59        26.99        17.29 
TCGA-QG-A5Z2 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       14.76        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       14.50         8.45        15.39        20.02        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3594 
        8.02         7.07         1.02         2.01        24.00         2.01 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        0.99        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.98         6.02        23.01        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
        1.02        31.00        70.03        64.01        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 
        0.69         0.72         1.81         6.05         6.05         9.37 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       12.00        15.02         7.10        30.05        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
      126.44        41.36        57.24        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 
       19.96        20.91        18.28        15.85        17.69         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       37.51        31.30         0.39         1.02         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        1.12         0.76        18.28        55.76 

  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                           0.26                            0.07 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE 
                          17.00                           18.05 
[1] "0.3 - 140.4 (17.0)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.1"
D51V2, continuous
D51V3, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED   102  50
  DEL PEAK 24(10Q23.31) WILD-TYPE 327 109
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED    102   50
  DEL PEAK 24(10Q23.31) WILD-TYPE  327  109
        clus
vv       DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  COLON                            102                             327
  RECTUM                            50                             109
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 24(10Q23.31) MUTATED        21        1        6        39         2
  DEL PEAK 24(10Q23.31) WILD-TYPE      81        0       30       126         8
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10Q23.31) MUTATED           1         6         10         19
  DEL PEAK 24(10Q23.31) WILD-TYPE         2        20         12         57
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 24(10Q23.31) MUTATED           16       22         6         1
  DEL PEAK 24(10Q23.31) WILD-TYPE         36       38        19         0
D51V4, multiclass
            clus
vv           DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  STAGE I                               21                              81
  STAGE IA                               1                               0
  STAGE II                               6                              30
  STAGE IIA                             39                             126
  STAGE IIB                              2                               8
  STAGE IIC                              1                               2
  STAGE III                              6                              20
  STAGE IIIA                            10                              12
  STAGE IIIB                            19                              57
  STAGE IIIC                            16                              36
  STAGE IV                              22                              38
  STAGE IVA                              6                              19
  STAGE IVB                              1                               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                              T0+T1  T2  T3  T4
  DEL PEAK 24(10Q23.31) MUTATED       3  24 109  15
  DEL PEAK 24(10Q23.31) WILD-TYPE    17  81 294  47
D51V5, multiclass
       clus
vv      DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  T0+T1                             3                              17
  T2                               24                              81
  T3                              109                             294
  T4                               15                              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 24(10Q23.31) MUTATED    75  43  34
  DEL PEAK 24(10Q23.31) WILD-TYPE 260 103  74
D51V6, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  N0                            75                             260
  N1                            43                             103
  N2                            34                              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 24(10Q23.31) MUTATED   113  25   2   1  10
  DEL PEAK 24(10Q23.31) WILD-TYPE 330  47   7   0  48
D51V7, multiclass
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  M0                            113                             330
  M1                             25                              47
  M1A                             2                               7
  M1B                             1                               0
  MX                             10                              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"
D51V8, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED    71  82
  DEL PEAK 24(10Q23.31) WILD-TYPE 206 233
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED     71   82
  DEL PEAK 24(10Q23.31) WILD-TYPE  206  233
        clus
vv       DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  FEMALE                            71                             206
  MALE                              82                             233
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                     94
  DEL PEAK 24(10Q23.31) WILD-TYPE                  279
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                               7
  DEL PEAK 24(10Q23.31) WILD-TYPE                            48
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                      41
  DEL PEAK 24(10Q23.31) WILD-TYPE                   102
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(10Q23.31) MUTATED                                7
  DEL PEAK 24(10Q23.31) WILD-TYPE                              6
D51V9, multiclass
                                clus
vv                               DEL PEAK 24(10Q23.31) MUTATED
  COLON ADENOCARCINOMA                                      94
  COLON MUCINOUS ADENOCARCINOMA                              7
  RECTAL ADENOCARCINOMA                                     41
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               DEL PEAK 24(10Q23.31) WILD-TYPE
  COLON ADENOCARCINOMA                                       279
  COLON MUCINOUS ADENOCARCINOMA                               48
  RECTAL ADENOCARCINOMA                                      102
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, binary
                                 cls
clus                                0   1
  DEL PEAK 24(10Q23.31) MUTATED     6 147
  DEL PEAK 24(10Q23.31) WILD-TYPE   3 436
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(10Q23.31) MUTATED      6  147
  DEL PEAK 24(10Q23.31) WILD-TYPE    3  436
     clus
vv    DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  NO                              6                               3
  YES                           147                             436
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 24(10Q23.31) MUTATED   112   1  12   5
  DEL PEAK 24(10Q23.31) WILD-TYPE 314   4  24  22
D51V11, multiclass
    clus
vv   DEL PEAK 24(10Q23.31) MUTATED DEL PEAK 24(10Q23.31) WILD-TYPE
  R0                           112                             314
  R1                             1                               4
  R2                            12                              24
  RX                             5                              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"
D51V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(10Q23.31) MUTATED                                  0     4
  DEL PEAK 24(10Q23.31) WILD-TYPE                                1     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(10Q23.31) MUTATED                          11    81
  DEL PEAK 24(10Q23.31) WILD-TYPE                        33   211
D51V13, multiclass
                                  clus
vv                                 DEL PEAK 24(10Q23.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                       81
                                  clus
vv                                 DEL PEAK 24(10Q23.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     33
  WHITE                                                        211
[1] 4 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 25(10Q25.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(10Q25.2) MUTATED   111  31
  DEL PEAK 25(10Q25.2) WILD-TYPE 346  75
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                           142                            421 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                            31                             75 
$`DEL PEAK 25(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-AF-2687 
       36.72        36.00        26.04        91.79        46.75        24.13 
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3593 
       17.95        13.55        12.72        10.39        32.02        34.03 
TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3909 
        6.05        29.98        36.95        17.03         1.02        19.99 
TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A01W 
       36.03        13.94        25.97        37.02        12.00        70.03 
TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-6155 
       10.98        41.00         4.60        10.19         4.73        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF 
       36.00        30.05        13.05        10.06       129.27        24.13 
TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6702 
        2.40        17.00        16.31        16.41        11.97        14.86 
TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
        0.66         0.46        47.08        26.43 

$`DEL PEAK 25(10Q25.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2682 
       46.65        43.76        43.43        23.38        44.91        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-A6-5656 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-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       22.09        22.06        27.09        24.13         8.38        25.08 
TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       24.16        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       20.28        16.24        24.92         1.02         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       38.99         1.02        24.03        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        34.03        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       14.01        21.01        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-3663 
       20.98        19.99        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 
        5.98        19.00        26.99        19.04         0.99        35.05 
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-3858 
       14.93        17.03         0.99        36.03        32.05        31.07 
TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3877 
       31.07        53.00        27.02        29.98        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 
        2.01        12.99        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-3973 
       20.98        34.03         2.01        21.99        16.08        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-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-A01C TCGA-AA-A01F 
       14.99        21.99        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-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        35.01        37.02        51.98         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        2.01         5.03        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-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        1.58         0.10         0.76         0.46         0.92        27.09 
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-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-5254 TCGA-CA-5255 
      100.01         5.23        11.74         1.94         2.24         3.06 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
        2.14         3.25         0.07         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-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.01         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 
       37.02        26.04        27.02        13.02        22.98        30.08 
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-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       12.95        13.05        11.01        12.03        14.99        12.26 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       19.59        13.51        11.51        20.19        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        1.32        15.12         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-D5-6932 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-A1DA 
       38.20       130.65        92.75        49.91        12.59         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-DM-A28M 
       81.37       119.93        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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        16.31        29.59         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-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 
       74.56        43.07        61.87        53.62        44.68        51.75 
TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 
       45.11        39.42        35.93        26.43        22.09        13.78 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V 
       35.80        26.17        47.15        52.80         4.11         5.06 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       17.23        43.04        19.10        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
        8.45        15.39        20.02        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99         1.02        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       48.03        32.02        28.04        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.98         6.02        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
        9.07         1.02        31.00        64.01        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72         1.81         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
       15.02        12.99        12.00        15.02         7.10        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        0.49        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46         8.45         9.96        37.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
        1.02         0.69         0.53         1.12         0.76        18.28 
TCGA-G5-6235 
       55.76 

  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE 
                        17.015                         18.050 
[1] "0.2 - 140.4 (17.0)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.3"
D52V2, continuous
D52V3, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED   103  46
  DEL PEAK 25(10Q25.2) WILD-TYPE 326 113
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED    103   46
  DEL PEAK 25(10Q25.2) WILD-TYPE  326  113
        clus
vv       DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  COLON                           103                            326
  RECTUM                           46                            113
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 25(10Q25.2) MUTATED        19        0        8        40         0
  DEL PEAK 25(10Q25.2) WILD-TYPE      83        1       28       125        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10Q25.2) MUTATED           1         7          7         18
  DEL PEAK 25(10Q25.2) WILD-TYPE         2        19         15         58
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 25(10Q25.2) MUTATED           18       22         6         0
  DEL PEAK 25(10Q25.2) WILD-TYPE         34       38        19         1
D52V4, multiclass
            clus
vv           DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  STAGE I                              19                             83
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            40                            125
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             7                             19
  STAGE IIIA                            7                             15
  STAGE IIIB                           18                             58
  STAGE IIIC                           18                             34
  STAGE IV                             22                             38
  STAGE IVA                             6                             19
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 25(10Q25.2) MUTATED       3  22 111  13
  DEL PEAK 25(10Q25.2) WILD-TYPE    17  83 292  49
D52V5, multiclass
       clus
vv      DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  T0+T1                            3                             17
  T2                              22                             83
  T3                             111                            292
  T4                              13                             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 25(10Q25.2) MUTATED    72  41  36
  DEL PEAK 25(10Q25.2) WILD-TYPE 263 105  72
D52V6, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  N0                           72                            263
  N1                           41                            105
  N2                           36                             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 25(10Q25.2) MUTATED   111  24   3   0  10
  DEL PEAK 25(10Q25.2) WILD-TYPE 332  48   6   1  48
D52V7, multiclass
     clus
vv    DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  M0                           111                            332
  M1                            24                             48
  M1A                            3                              6
  M1B                            0                              1
  MX                            10                             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"
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED    70  80
  DEL PEAK 25(10Q25.2) WILD-TYPE 207 235
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED     70   80
  DEL PEAK 25(10Q25.2) WILD-TYPE  207  235
        clus
vv       DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  FEMALE                           70                            207
  MALE                             80                            235
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                     95
  DEL PEAK 25(10Q25.2) WILD-TYPE                  278
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                               8
  DEL PEAK 25(10Q25.2) WILD-TYPE                            47
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                      38
  DEL PEAK 25(10Q25.2) WILD-TYPE                   105
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(10Q25.2) MUTATED                                7
  DEL PEAK 25(10Q25.2) WILD-TYPE                              6
D52V9, multiclass
                                clus
vv                               DEL PEAK 25(10Q25.2) MUTATED
  COLON ADENOCARCINOMA                                     95
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    38
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK 25(10Q25.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      278
  COLON MUCINOUS ADENOCARCINOMA                              47
  RECTAL ADENOCARCINOMA                                     105
  RECTAL MUCINOUS ADENOCARCINOMA                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, binary
                                cls
clus                               0   1
  DEL PEAK 25(10Q25.2) MUTATED     6 144
  DEL PEAK 25(10Q25.2) WILD-TYPE   3 439
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(10Q25.2) MUTATED      6  144
  DEL PEAK 25(10Q25.2) WILD-TYPE    3  439
     clus
vv    DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  NO                             6                              3
  YES                          144                            439
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(10Q25.2) MUTATED   109   1  12   5
  DEL PEAK 25(10Q25.2) WILD-TYPE 317   4  24  22
D52V11, multiclass
    clus
vv   DEL PEAK 25(10Q25.2) MUTATED DEL PEAK 25(10Q25.2) WILD-TYPE
  R0                          109                            317
  R1                            1                              4
  R2                           12                             24
  RX                            5                             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"
D52V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 25(10Q25.2) MUTATED                                  0     3
  DEL PEAK 25(10Q25.2) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(10Q25.2) MUTATED                          11    77
  DEL PEAK 25(10Q25.2) WILD-TYPE                        33   215
D52V13, multiclass
                                  clus
vv                                 DEL PEAK 25(10Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                      77
                                  clus
vv                                 DEL PEAK 25(10Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    33
  WHITE                                                       215
[1] 4 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 26(11Q22.3) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(11Q22.3) MUTATED    83  20
  DEL PEAK 26(11Q22.3) WILD-TYPE 374  86
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                           103                            460 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                            20                             86 
$`DEL PEAK 26(11Q22.3) MUTATED`
TCGA-A6-2671 TCGA-A6-2681 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 
       37.02        45.60        15.52        36.53        32.45        30.44 
TCGA-A6-6138 TCGA-A6-6649 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3511 
       22.52        24.16        21.76        23.87         5.03         6.97 
TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3558 TCGA-AA-3662 TCGA-AA-3666 TCGA-AA-3680 
        9.07        37.05        20.98         6.05         2.01        11.01 
TCGA-AA-3692 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       36.00        32.05        31.07        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3972 TCGA-AA-A00F 
        2.01        34.03         2.01        21.99        50.99        34.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A03J 
       42.02        32.02        33.04         2.96        39.98        40.96 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 
        1.58         1.02         0.43        14.50         0.95        15.75 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4323 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4951 
        0.20         5.52         1.41         2.14         0.26        70.16 
TCGA-CK-6748 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6163 
        2.01        30.08         5.03        15.02        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6536 TCGA-D5-6924 
       11.01        11.01        14.99        20.19        17.85        14.30 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-F4-6461 TCGA-G4-6315 TCGA-G4-6317 
      130.65        49.91         7.50        11.11        36.72        36.00 
TCGA-G4-6626 TCGA-NH-A50T TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
       46.75         4.11        43.04        13.55        19.10        14.50 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3593 
       15.39        10.39        32.02         7.07        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3896 TCGA-AG-A008 
        2.01         6.05         0.99        32.98         1.02        13.94 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 
       12.00        70.03        64.01        10.98        41.00         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6158 
        0.69         0.72        10.19        13.97        13.97         7.10 
TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6881 
       30.05         5.29        24.13        20.91        17.00        16.41 
TCGA-EI-7004 
        8.45 

$`DEL PEAK 26(11Q22.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       16.04        34.65        14.53        32.91        31.63        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-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       27.09        24.13         8.38        25.08        25.18        20.61 
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-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-3514 TCGA-AA-3516 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 
        1.02        13.02        38.99         1.02        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-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-3560 
       13.02        24.00        17.95        29.95        23.01        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-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-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-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-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3955 
       31.00         2.01        33.01        26.01        24.00        20.98 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
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-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-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02         0.99        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X 
       38.07         1.02        35.01         1.02        35.01        26.01 
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-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-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-6004 TCGA-AY-4070 TCGA-AY-6197 
        0.20         0.46         0.92        27.09        16.31        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4614 
       17.82         5.19        75.25        50.37        58.39         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-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-4948 TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5912 TCGA-CK-5913 
       17.56       102.44        40.34        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        21.01         2.93       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-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 
       29.06        22.03        22.98        16.01        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        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-6675 
       12.99        13.02        15.02        14.04        12.95        13.05 
TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       11.08        11.08        10.06        12.03        12.26        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       13.51        11.51        20.42        17.75        18.25         1.32 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        15.12         4.50        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         1.51        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D7 
       10.26       119.70        24.43        38.20        92.75        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-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       13.38        13.64        13.45         6.18        35.87         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-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-G4-6298 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-G4-6320 
       55.04        51.75        45.11        39.42        35.93        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       22.09        26.04        13.78        35.80        26.17        91.79 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       47.15        52.80         5.06         2.79         5.98         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       26.99        17.29        14.76        24.13        17.95        17.23 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 
       12.72        37.74        10.39         8.45        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         8.02         1.02         2.01        24.00         1.02 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        7.99        29.98         1.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03         0.99        20.98         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       31.00        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       38.04         1.45         4.60         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37         4.73        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        12.00        15.02        36.00 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       19.96        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                        130.65                         140.38 
  DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE 
                        15.020                         18.265 
[1] "0.2 - 130.7 (15.0)" "0.1 - 140.4 (18.3)"
[1] "hr=" "1.3"
D53V2, continuous
D53V3, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    69  36
  DEL PEAK 26(11Q22.3) WILD-TYPE 360 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     69   36
  DEL PEAK 26(11Q22.3) WILD-TYPE  360  123
        clus
vv       DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  COLON                            69                            360
  RECTUM                           36                            123
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 26(11Q22.3) MUTATED        21        0        4        26         0
  DEL PEAK 26(11Q22.3) WILD-TYPE      81        1       32       139        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(11Q22.3) MUTATED           0         6          4         14
  DEL PEAK 26(11Q22.3) WILD-TYPE         3        20         18         62
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 26(11Q22.3) MUTATED           11       14         6         0
  DEL PEAK 26(11Q22.3) WILD-TYPE         41       46        19         1
D53V4, multiclass
            clus
vv           DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  STAGE I                              21                             81
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            26                            139
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             6                             20
  STAGE IIIA                            4                             18
  STAGE IIIB                           14                             62
  STAGE IIIC                           11                             41
  STAGE IV                             14                             46
  STAGE IVA                             6                             19
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 26(11Q22.3) MUTATED       4  18  73  14
  DEL PEAK 26(11Q22.3) WILD-TYPE    16  87 330  48
D53V5, multiclass
       clus
vv      DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  T0+T1                            4                             16
  T2                              18                             87
  T3                              73                            330
  T4                              14                             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 26(11Q22.3) MUTATED    54  32  22
  DEL PEAK 26(11Q22.3) WILD-TYPE 281 114  86
D53V6, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  N0                           54                            281
  N1                           32                            114
  N2                           22                             86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 26(11Q22.3) MUTATED    76  15   3   0  12
  DEL PEAK 26(11Q22.3) WILD-TYPE 367  57   6   1  46
D53V7, multiclass
     clus
vv    DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  M0                            76                            367
  M1                            15                             57
  M1A                            3                              6
  M1B                            0                              1
  MX                            12                             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"
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED    54  55
  DEL PEAK 26(11Q22.3) WILD-TYPE 223 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED     54   55
  DEL PEAK 26(11Q22.3) WILD-TYPE  223  260
        clus
vv       DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  FEMALE                           54                            223
  MALE                             55                            260
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                     61
  DEL PEAK 26(11Q22.3) WILD-TYPE                  312
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                               8
  DEL PEAK 26(11Q22.3) WILD-TYPE                            47
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                      29
  DEL PEAK 26(11Q22.3) WILD-TYPE                   114
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(11Q22.3) MUTATED                                6
  DEL PEAK 26(11Q22.3) WILD-TYPE                              7
D53V9, multiclass
                                clus
vv                               DEL PEAK 26(11Q22.3) MUTATED
  COLON ADENOCARCINOMA                                     61
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    29
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 26(11Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      312
  COLON MUCINOUS ADENOCARCINOMA                              47
  RECTAL ADENOCARCINOMA                                     114
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, binary
                                cls
clus                               0   1
  DEL PEAK 26(11Q22.3) MUTATED     3 106
  DEL PEAK 26(11Q22.3) WILD-TYPE   6 477
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(11Q22.3) MUTATED      3  106
  DEL PEAK 26(11Q22.3) WILD-TYPE    6  477
     clus
vv    DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  NO                             3                              6
  YES                          106                            477
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(11Q22.3) MUTATED    76   1   9   4
  DEL PEAK 26(11Q22.3) WILD-TYPE 350   4  27  23
D53V11, multiclass
    clus
vv   DEL PEAK 26(11Q22.3) MUTATED DEL PEAK 26(11Q22.3) WILD-TYPE
  R0                           76                            350
  R1                            1                              4
  R2                            9                             27
  RX                            4                             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"
D53V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 26(11Q22.3) MUTATED                                  0     3
  DEL PEAK 26(11Q22.3) WILD-TYPE                                1     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(11Q22.3) MUTATED                           4    54
  DEL PEAK 26(11Q22.3) WILD-TYPE                        40   238
D53V13, multiclass
                                  clus
vv                                 DEL PEAK 26(11Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      54
                                  clus
vv                                 DEL PEAK 26(11Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    40
  WHITE                                                       238
[1] 4 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 27(12P13.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(12P13.1) MUTATED    61  21
  DEL PEAK 27(12P13.1) WILD-TYPE 396  85
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            82                            481 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                            21                             85 
$`DEL PEAK 27(12P13.1) 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-3544 
       24.69        20.28        61.84         9.63        26.01        14.01 
TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3688 
       33.99        13.02        78.08         2.01        50.04        19.00 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-A01F 
       31.07        17.03        24.03         2.01        50.99        32.02 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AZ-4684 
       33.04         2.96         1.58         1.02         0.43        65.00 
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-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-F4-6460 
       15.12         7.53        11.38        13.32        12.59        13.38 
TCGA-F4-6461 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6586 
       11.11        16.24        61.87        36.72        36.00        35.80 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       43.04        13.55        19.10        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3898 
       20.02        36.03        34.03        29.98         1.02        48.03 
TCGA-AG-A00C TCGA-AG-A01W TCGA-AG-A026 TCGA-AH-6544 TCGA-CI-6620 TCGA-DC-6155 
        6.02        70.03         1.94         0.49         6.05        13.97 
TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6514 
        7.10        24.13        51.48        20.91        17.00        16.31 
TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6641 
       16.41        14.86         0.66        26.43 

$`DEL PEAK 27(12P13.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
        5.06        46.65        43.76        43.43        23.38        42.28 
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-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       16.04        14.53        32.45        32.91        31.63        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-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       24.16        20.61        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 
       19.66        16.24        24.92        52.44         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-3542 TCGA-AA-3543 
       19.07        34.03        29.00        29.00        12.99         0.99 
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-3662 TCGA-AA-3663 
       19.99        13.94        19.99        61.02         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 
       11.01         5.98        37.05        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-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        31.07        53.00        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-3966 TCGA-AA-3968 
       26.01        24.00        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 
       16.08        13.05        34.06        26.01        25.02        24.00 
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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       21.99        34.98        15.02        15.02         0.99        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-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        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-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-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 
        0.79         0.72         0.10         0.76         0.20         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 
        0.20        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-4616 
       50.37        58.39         1.41         5.65        32.94         5.13 
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-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-5796 TCGA-CA-5797 TCGA-CA-6716 
        1.94         2.24         3.06         3.25         3.29         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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.01         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-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04        27.02        13.02        29.06        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01        15.02        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-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       13.02        14.04        12.95        13.05        11.08        11.01 
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-D5-6531 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-D5-6538 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-D5-6926 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-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20       130.65        92.75        49.91       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-F4-6463 TCGA-F4-6569 
      117.07        98.24        95.18         8.61        13.64        13.45 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
        6.18        35.87         1.55        16.31        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-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
        8.35        82.39        23.51        74.56        43.07        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-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6588 TCGA-G4-6625 
       26.43        22.09        26.04        13.78        26.17        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       46.75        47.15        52.80         4.11         5.06         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 
        5.98         5.59        26.99        17.29        14.76        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6672 
       17.95        17.23        12.72        37.74         8.45        10.39 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        0.99        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         0.99        20.98        13.94        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G 
       31.00        64.01        10.98        51.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.04         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81        10.19         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       15.02        12.99        12.00        15.02        36.00        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       57.24       129.27        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 
       19.96        18.28        15.85        17.69        16.34         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
        9.96        37.51        31.30         0.39         1.02         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                         78.08                         140.38 
  DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE 
                         16.36                          18.05 
[1] "0.1 - 78.1 (16.4)"  "0.1 - 140.4 (18.1)"
[1] "hr=" "1.6"
D54V2, continuous
D54V3, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    54  29
  DEL PEAK 27(12P13.1) WILD-TYPE 375 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     54   29
  DEL PEAK 27(12P13.1) WILD-TYPE  375  130
        clus
vv       DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  COLON                            54                            375
  RECTUM                           29                            130
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 27(12P13.1) MUTATED        13        0        5        16         1
  DEL PEAK 27(12P13.1) WILD-TYPE      89        1       31       149         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(12P13.1) MUTATED           0         2          5         11
  DEL PEAK 27(12P13.1) WILD-TYPE         3        24         17         65
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 27(12P13.1) MUTATED           12       11         7         0
  DEL PEAK 27(12P13.1) WILD-TYPE         40       49        18         1
D54V4, multiclass
            clus
vv           DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  STAGE I                              13                             89
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            16                            149
  STAGE IIB                             1                              9
  STAGE IIC                             0                              3
  STAGE III                             2                             24
  STAGE IIIA                            5                             17
  STAGE IIIB                           11                             65
  STAGE IIIC                           12                             40
  STAGE IV                             11                             49
  STAGE IVA                             7                             18
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 27(12P13.1) MUTATED       4  13  63   6
  DEL PEAK 27(12P13.1) WILD-TYPE    16  92 340  56
D54V5, multiclass
       clus
vv      DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  T0+T1                            4                             16
  T2                              13                             92
  T3                              63                            340
  T4                               6                             56
[1] 4 2
[1] TRUE
[1] "dimension 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(12P13.1) MUTATED    38  31  17
  DEL PEAK 27(12P13.1) WILD-TYPE 297 115  91
D54V6, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  N0                           38                            297
  N1                           31                            115
  N2                           17                             91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 27(12P13.1) MUTATED    56  17   1   0  11
  DEL PEAK 27(12P13.1) WILD-TYPE 387  55   8   1  47
D54V7, multiclass
     clus
vv    DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  M0                            56                            387
  M1                            17                             55
  M1A                            1                              8
  M1B                            0                              1
  MX                            11                             47
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED    42  44
  DEL PEAK 27(12P13.1) WILD-TYPE 235 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED     42   44
  DEL PEAK 27(12P13.1) WILD-TYPE  235  271
        clus
vv       DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  FEMALE                           42                            235
  MALE                             44                            271
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                     53
  DEL PEAK 27(12P13.1) WILD-TYPE                  320
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                               1
  DEL PEAK 27(12P13.1) WILD-TYPE                            54
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                      28
  DEL PEAK 27(12P13.1) WILD-TYPE                   115
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(12P13.1) MUTATED                                1
  DEL PEAK 27(12P13.1) WILD-TYPE                             12
D54V9, multiclass
                                clus
vv                               DEL PEAK 27(12P13.1) MUTATED
  COLON ADENOCARCINOMA                                     53
  COLON MUCINOUS ADENOCARCINOMA                             1
  RECTAL ADENOCARCINOMA                                    28
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 27(12P13.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      320
  COLON MUCINOUS ADENOCARCINOMA                              54
  RECTAL ADENOCARCINOMA                                     115
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D54V10, binary
                                cls
clus                               0   1
  DEL PEAK 27(12P13.1) MUTATED     2  84
  DEL PEAK 27(12P13.1) WILD-TYPE   7 499
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(12P13.1) MUTATED      2   84
  DEL PEAK 27(12P13.1) WILD-TYPE    7  499
     clus
vv    DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  NO                             2                              7
  YES                           84                            499
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(12P13.1) MUTATED    61   1   6   4
  DEL PEAK 27(12P13.1) WILD-TYPE 365   4  30  23
D54V11, multiclass
    clus
vv   DEL PEAK 27(12P13.1) MUTATED DEL PEAK 27(12P13.1) WILD-TYPE
  R0                           61                            365
  R1                            1                              4
  R2                            6                             30
  RX                            4                             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"
D54V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 27(12P13.1) MUTATED                                  0     2
  DEL PEAK 27(12P13.1) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(12P13.1) MUTATED                           5    51
  DEL PEAK 27(12P13.1) WILD-TYPE                        39   241
D54V13, multiclass
                                  clus
vv                                 DEL PEAK 27(12P13.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      51
                                  clus
vv                                 DEL PEAK 27(12P13.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       241
[1] 4 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 28(12Q21.33) MUTATION ANALYSIS
D55V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 28(12Q21.33) MUTATED    63  19
  DEL PEAK 28(12Q21.33) WILD-TYPE 394  87
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             82                             481 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                             19                              87 
$`DEL PEAK 28(12Q21.33) MUTATED`
TCGA-A6-2671 TCGA-A6-2677 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5662 
       37.02        17.79        34.65        36.53        30.44        23.61 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3542 
       20.28        61.84        52.44         9.63        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3673 
       14.01        33.99        13.02        17.95        23.01        50.04 
TCGA-AA-3685 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3968 
       37.05        31.07        17.03        24.03         2.01        21.99 
TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 
       50.99        24.00        32.02        33.04         2.96         1.58 
TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-6607 TCGA-CA-5256 
        1.02         0.43        14.50         0.20         3.19         2.14 
TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6163 
        0.26        48.20         8.02        29.06         5.03        14.04 
TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6677 TCGA-D5-6533 
       29.03        15.02        11.01        13.05        11.08         1.32 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-F4-6460 TCGA-F4-6807 
       13.41        11.38        12.59         7.50        13.38        16.24 
TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-4110 
       61.87        36.72        36.00        43.04        12.72        14.50 
TCGA-AF-6136 TCGA-AG-3574 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3898 
       15.39        36.03        34.03        29.98        32.98        48.03 
TCGA-AG-4001 TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A032 TCGA-AH-6544 TCGA-DC-6155 
       36.03        23.01        15.95        38.04         0.49        13.97 
TCGA-DC-6158 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 
        7.10       129.27        24.13        17.00        16.31        16.41 
TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6233 
       11.51        14.86         0.66        18.28 

$`DEL PEAK 28(12Q21.33) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
        5.06        46.65        43.76        43.43        23.38        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        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-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        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-A565 TCGA-A6-A566 TCGA-AA-3488 TCGA-AA-3489 
       20.12        19.66        16.24        24.92         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-3543 TCGA-AA-3549 
       19.07        34.03        29.00        29.00         0.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 
       24.00        29.95        20.98        19.99        13.94        19.99 
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-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        19.00        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-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-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 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-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-3971 TCGA-AA-3973 
       24.00        20.98        34.03         2.01        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3989 
       34.06        26.01        25.02        27.02        19.07         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       18.05        18.05        17.03         4.01        27.02        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-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-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-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
        0.76         0.20         0.46         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-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-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-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-4948 
        0.07         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        21.01 
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-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
        8.02        26.04        27.02        13.02        22.03        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       30.08        16.01        15.02        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-6674 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       13.02        14.04        12.95        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-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       20.19        20.42        17.75        18.25         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
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-D5-6927 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-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-F4-6461 
       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-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        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-G4-6299 
      107.67        28.21         8.35        82.39        23.51        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6310 
       43.07        53.62        44.68        55.04        51.75        45.11 
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-G4-6625 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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV 
        4.11         5.06         2.79         5.98         5.59        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       17.29        14.76        24.13        17.95        17.23        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       19.10        37.74        10.39         8.45        20.02        10.39 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        0.99         1.02         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
        0.99        20.98        13.94         6.02        25.97        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       61.97        41.00         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       15.02        12.99        12.00        15.02        36.00        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       57.24        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        18.28        15.85        17.69        16.34 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
        9.96        37.51        31.30         0.39         1.02         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                           0.20                            0.07 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                         129.27                          140.38 
  DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE 
                         17.015                          18.050 
[1] "0.2 - 129.3 (17.0)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.4"
D55V2, continuous
D55V3, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    57  27
  DEL PEAK 28(12Q21.33) WILD-TYPE 372 132
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     57   27
  DEL PEAK 28(12Q21.33) WILD-TYPE  372  132
        clus
vv       DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  COLON                             57                             372
  RECTUM                            27                             132
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 28(12Q21.33) MUTATED        15        0        3        19         1
  DEL PEAK 28(12Q21.33) WILD-TYPE      87        1       33       146         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(12Q21.33) MUTATED           2         1          4          9
  DEL PEAK 28(12Q21.33) WILD-TYPE         1        25         18         67
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 28(12Q21.33) MUTATED           14        9         4         1
  DEL PEAK 28(12Q21.33) WILD-TYPE         38       51        21         0
D55V4, multiclass
            clus
vv           DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  STAGE I                               15                              87
  STAGE IA                               0                               1
  STAGE II                               3                              33
  STAGE IIA                             19                             146
  STAGE IIB                              1                               9
  STAGE IIC                              2                               1
  STAGE III                              1                              25
  STAGE IIIA                             4                              18
  STAGE IIIB                             9                              67
  STAGE IIIC                            14                              38
  STAGE IV                               9                              51
  STAGE IVA                              4                              21
  STAGE IVB                              1                               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                              T0+T1  T2  T3  T4
  DEL PEAK 28(12Q21.33) MUTATED       3  15  62   5
  DEL PEAK 28(12Q21.33) WILD-TYPE    17  90 341  57
D55V5, multiclass
       clus
vv      DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  T0+T1                             3                              17
  T2                               15                              90
  T3                               62                             341
  T4                                5                              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"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 28(12Q21.33) MUTATED    41  23  21
  DEL PEAK 28(12Q21.33) WILD-TYPE 294 123  87
D55V6, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  N0                            41                             294
  N1                            23                             123
  N2                            21                              87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1 M1A M1B  MX
  DEL PEAK 28(12Q21.33) MUTATED    61  12   1   1   8
  DEL PEAK 28(12Q21.33) WILD-TYPE 382  60   8   0  50
D55V7, multiclass
     clus
vv    DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  M0                             61                             382
  M1                             12                              60
  M1A                             1                               8
  M1B                             1                               0
  MX                              8                              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"
D55V8, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED    39  46
  DEL PEAK 28(12Q21.33) WILD-TYPE 238 269
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED     39   46
  DEL PEAK 28(12Q21.33) WILD-TYPE  238  269
        clus
vv       DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  FEMALE                            39                             238
  MALE                              46                             269
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                     54
  DEL PEAK 28(12Q21.33) WILD-TYPE                  319
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                               2
  DEL PEAK 28(12Q21.33) WILD-TYPE                            53
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                      26
  DEL PEAK 28(12Q21.33) WILD-TYPE                   117
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(12Q21.33) MUTATED                                1
  DEL PEAK 28(12Q21.33) WILD-TYPE                             12
D55V9, multiclass
                                clus
vv                               DEL PEAK 28(12Q21.33) MUTATED
  COLON ADENOCARCINOMA                                      54
  COLON MUCINOUS ADENOCARCINOMA                              2
  RECTAL ADENOCARCINOMA                                     26
  RECTAL MUCINOUS ADENOCARCINOMA                             1
                                clus
vv                               DEL PEAK 28(12Q21.33) WILD-TYPE
  COLON ADENOCARCINOMA                                       319
  COLON MUCINOUS ADENOCARCINOMA                               53
  RECTAL ADENOCARCINOMA                                      117
  RECTAL MUCINOUS ADENOCARCINOMA                              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"
D55V10, binary
                                 cls
clus                                0   1
  DEL PEAK 28(12Q21.33) MUTATED     2  83
  DEL PEAK 28(12Q21.33) WILD-TYPE   7 500
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(12Q21.33) MUTATED      2   83
  DEL PEAK 28(12Q21.33) WILD-TYPE    7  500
     clus
vv    DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  NO                              2                               7
  YES                            83                             500
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 28(12Q21.33) MUTATED    67   0   3   3
  DEL PEAK 28(12Q21.33) WILD-TYPE 359   5  33  24
D55V11, multiclass
    clus
vv   DEL PEAK 28(12Q21.33) MUTATED DEL PEAK 28(12Q21.33) WILD-TYPE
  R0                            67                             359
  R1                             0                               5
  R2                             3                              33
  RX                             3                              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"
D55V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 28(12Q21.33) MUTATED                                  0     2
  DEL PEAK 28(12Q21.33) WILD-TYPE                                1    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(12Q21.33) MUTATED                           5    47
  DEL PEAK 28(12Q21.33) WILD-TYPE                        39   245
D55V13, multiclass
                                  clus
vv                                 DEL PEAK 28(12Q21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                    5
  WHITE                                                       47
                                  clus
vv                                 DEL PEAK 28(12Q21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     39
  WHITE                                                        245
[1] 4 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 29(14Q11.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(14Q11.2) MUTATED   157  35
  DEL PEAK 29(14Q11.2) WILD-TYPE 300  71
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                           192                            371 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                            35                             71 
$`DEL PEAK 29(14Q11.2) MUTATED`
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       37.02        42.28        35.11        15.52        34.65        36.53 
TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6138 
       14.53        32.45        32.91        30.44        23.61        22.52 
TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       24.13        25.08        20.61        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3511 TCGA-AA-3517 
       20.28        61.84         5.03         1.02         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
        9.07        24.03        36.03        19.07        34.03        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3666 TCGA-AA-3667 
       23.01        19.99        13.94        19.99         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3811 
       50.04        47.01        37.05        19.00        85.05         0.99 
TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3866 TCGA-AA-3867 
       25.02        36.95        37.02        17.03        17.03        24.03 
TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       18.05        12.99        34.03        21.99        16.08        50.99 
TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O 
       34.06        26.01         7.96        34.03        17.03        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K 
       42.02        14.99        21.99        15.02        32.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 
       33.04        26.01         2.96         2.01        40.96         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 
        1.02         0.10         0.43        14.50         0.95        15.75 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 
        5.52        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-6172 TCGA-CM-6676 TCGA-CM-6679 
       29.03        13.02        15.02        11.01        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-A1D8 TCGA-DM-A1D9 
       14.30        13.41        11.38        38.20        12.59       140.38 
TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28E TCGA-F4-6460 TCGA-F4-6806 TCGA-F4-6808 
        6.12        14.04       119.93        13.38        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 
        1.28         0.53        28.21         8.35        82.39        36.72 
TCGA-G4-6625 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-AF-2689 TCGA-AF-2692 
       91.79         4.11         5.06         5.59        17.95        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3581 
       19.10        12.72        37.74        10.39        36.03         7.07 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3882 
       34.03        50.04         6.05         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
        1.02        17.03        35.01         1.02        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A026 
       14.04        17.03         6.02        25.97        23.01         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
       38.96        38.04         0.49        10.19         6.05         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 
        9.37         4.73        13.97         7.99        11.01        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
       13.97        36.00         7.10        13.05        10.06       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6513 
       24.13        51.48        20.55        20.91        17.00        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 
       16.31        16.41        10.78        11.97        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        1.02         0.66         0.76        18.28        55.76        26.43 

$`DEL PEAK 29(14Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2679 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        45.60        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-A6-6649 TCGA-A6-6653 
       29.16        27.09         8.38        25.18        24.16        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.12        19.66        16.24        24.92        52.44         9.63 
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-3525 
       63.98         1.02        13.02         1.02        37.05         8.05 
TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       19.07        29.00        29.00        26.01        12.99         0.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       14.01        33.99        21.01        24.00        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 
       20.98        61.02        78.08         6.05         6.97        54.02 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 
        0.92        47.05        15.02        11.01         5.98        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-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 
        1.02        17.98        15.95        38.99        14.93         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-3869 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        29.98        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3966 
       33.01        26.01        24.00         2.01        20.98         2.01 
TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 
       13.05        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-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D 
        4.01         0.99        17.03        34.98        15.02         0.99 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       12.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J 
       35.01        37.02        39.06        51.98        39.98         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05         0.07 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6964 
       21.37         4.21        56.55         0.79         0.72         0.76 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 
        0.20         0.46         0.92        27.09        16.31         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 
       21.44        17.82         5.19        50.37        58.39        32.94 
TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        83.80        65.00        62.79        61.41        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        12.10       100.01        11.74         3.19         2.24 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.25         3.29         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-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.01         2.93       124.27        23.05        20.02        37.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       26.04        27.02        13.02        29.06        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-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-CM-6680 
       14.04        12.95        13.05        11.08        11.01        12.03 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 
       19.59        11.51        20.19        20.42        17.75         7.92 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        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-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1DB 
      130.65        92.75        49.91        13.32         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      131.51       135.65         7.76       139.17        26.47        81.37 
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-F4-6461 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-G4-6298 
       16.31        16.24        35.41        19.43       107.67        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-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6320 
       51.75        45.11        39.42        35.93        36.00        26.43 
TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 
       22.09        26.04        13.78        35.80        26.17        46.75 
TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YX 
       47.15        52.80         2.79         5.98        26.99        17.29 
TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3913 TCGA-AF-4110 
       14.76        24.13        17.23        43.04        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
        8.45        15.39        20.02        12.00        32.02         8.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
        1.02         2.01        24.00         1.02        46.03         2.01 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 
       29.98         1.02        32.98         0.99        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4007 TCGA-AG-4022 
       14.01        48.03        32.02        19.99         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.98        13.94        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 
       51.98        49.97        61.97        41.00         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 
        0.72         4.60         1.81         6.97        60.03        10.98 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       15.02        12.00        15.02        30.05        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      126.44        41.36        57.24        32.61         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
       19.96        18.28        15.85        17.69         8.61        11.51 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       13.64        17.46         8.45         9.96        37.51        14.86 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
        0.69         0.53         1.12         0.46        47.08 

  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE 
                        16.705                         19.040 
[1] "0.1 - 140.4 (16.7)" "0.1 - 139.2 (19.0)"
[1] "hr=" "1.2"
D56V2, continuous
D56V3, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED   131  66
  DEL PEAK 29(14Q11.2) WILD-TYPE 298  93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED    131   66
  DEL PEAK 29(14Q11.2) WILD-TYPE  298   93
        clus
vv       DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  COLON                           131                            298
  RECTUM                           66                             93
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 29(14Q11.2) MUTATED        32        0       11        52         1
  DEL PEAK 29(14Q11.2) WILD-TYPE      70        1       25       113         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(14Q11.2) MUTATED           1         9         10         27
  DEL PEAK 29(14Q11.2) WILD-TYPE         2        17         12         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 29(14Q11.2) MUTATED           17       24        11         0
  DEL PEAK 29(14Q11.2) WILD-TYPE         35       36        14         1
D56V4, multiclass
            clus
vv           DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  STAGE I                              32                             70
  STAGE IA                              0                              1
  STAGE II                             11                             25
  STAGE IIA                            52                            113
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                             9                             17
  STAGE IIIA                           10                             12
  STAGE IIIB                           27                             49
  STAGE IIIC                           17                             35
  STAGE IV                             24                             36
  STAGE IVA                            11                             14
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 29(14Q11.2) MUTATED       9  33 142  16
  DEL PEAK 29(14Q11.2) WILD-TYPE    11  72 261  46
D56V5, multiclass
       clus
vv      DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  T0+T1                            9                             11
  T2                              33                             72
  T3                             142                            261
  T4                              16                             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
  DEL PEAK 29(14Q11.2) MUTATED   104  63  33
  DEL PEAK 29(14Q11.2) WILD-TYPE 231  83  75
D56V6, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  N0                          104                            231
  N1                           63                             83
  N2                           33                             75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 29(14Q11.2) MUTATED   144  32   3   0  18
  DEL PEAK 29(14Q11.2) WILD-TYPE 299  40   6   1  40
D56V7, multiclass
     clus
vv    DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  M0                           144                            299
  M1                            32                             40
  M1A                            3                              6
  M1B                            0                              1
  MX                            18                             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"
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED    94 106
  DEL PEAK 29(14Q11.2) WILD-TYPE 183 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED     94  106
  DEL PEAK 29(14Q11.2) WILD-TYPE  183  209
        clus
vv       DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  FEMALE                           94                            183
  MALE                            106                            209
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                    125
  DEL PEAK 29(14Q11.2) WILD-TYPE                  248
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                               5
  DEL PEAK 29(14Q11.2) WILD-TYPE                            50
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                      64
  DEL PEAK 29(14Q11.2) WILD-TYPE                    79
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(14Q11.2) MUTATED                                2
  DEL PEAK 29(14Q11.2) WILD-TYPE                             11
D56V9, multiclass
                                clus
vv                               DEL PEAK 29(14Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    125
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    64
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 29(14Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      248
  COLON MUCINOUS ADENOCARCINOMA                              50
  RECTAL ADENOCARCINOMA                                      79
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D56V10, binary
                                cls
clus                               0   1
  DEL PEAK 29(14Q11.2) MUTATED     4 196
  DEL PEAK 29(14Q11.2) WILD-TYPE   5 387
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(14Q11.2) MUTATED      4  196
  DEL PEAK 29(14Q11.2) WILD-TYPE    5  387
     clus
vv    DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  NO                             4                              5
  YES                          196                            387
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(14Q11.2) MUTATED   140   2  10   9
  DEL PEAK 29(14Q11.2) WILD-TYPE 286   3  26  18
D56V11, multiclass
    clus
vv   DEL PEAK 29(14Q11.2) MUTATED DEL PEAK 29(14Q11.2) WILD-TYPE
  R0                          140                            286
  R1                            2                              3
  R2                           10                             26
  RX                            9                             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"
D56V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 29(14Q11.2) MUTATED                                  0     4
  DEL PEAK 29(14Q11.2) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(14Q11.2) MUTATED                          13   101
  DEL PEAK 29(14Q11.2) WILD-TYPE                        31   191
D56V13, multiclass
                                  clus
vv                                 DEL PEAK 29(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                     101
                                  clus
vv                                 DEL PEAK 29(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    31
  WHITE                                                       191
[1] 4 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 30(14Q31.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(14Q31.1) MUTATED   162  34
  DEL PEAK 30(14Q31.1) WILD-TYPE 295  72
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                           196                            367 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                            34                             72 
$`DEL PEAK 30(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-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 
       75.25         1.41         5.65        22.36        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5912 
        1.94         3.06         2.14         0.07         0.26        48.20 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
        2.01         8.02         8.02        17.03        14.04        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 
       13.02        15.02        13.05        11.08        10.06        14.99 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 
       12.26        13.51        18.25         1.32        15.12        14.30 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
       13.41        11.38        38.20        13.32       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28E TCGA-F4-6460 TCGA-F4-6806 TCGA-F4-6808 
      131.51        14.04       119.93        13.38        29.59        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 TCGA-G4-6625 
        1.28         0.53         8.35        82.39        36.72        91.79 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3911 
        4.11         5.06         5.59        17.95        13.55        37.74 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03        50.04        12.03         6.05 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 
        0.99         1.02         0.99         1.02        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C 
        1.02        48.03        36.03        14.04        17.03         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       25.97        23.01        70.03         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 
        0.49        10.19         6.05         6.05         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
       13.97         7.99        10.98        11.01        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG 
       36.00         7.10        13.05        10.06       129.27        51.48 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       20.55        17.00        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       10.78        11.97        31.30         0.39         1.02         0.66 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.76        18.28        55.76        26.43 

$`DEL PEAK 30(14Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       44.91        13.94        37.05        37.25        16.04        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       27.09         8.38        25.18        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        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-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02        13.02         1.02        37.05        36.03         8.05 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01         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-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       61.02        78.08         6.05         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       47.05        11.01         5.98        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04         0.99        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       15.95        38.99        14.93         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        31.07        53.00        27.02        29.98 
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-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
       34.03         2.01        13.05        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 
       18.05        18.05         4.01         0.99        17.03        34.98 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02         0.99        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-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.72         0.76         0.20         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 
       16.31        21.44        17.82         5.19        50.37        58.39 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        83.80        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.24         3.25         3.29         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        21.01         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       37.02        26.04        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-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-6172 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 
       12.99        14.04        11.01        12.95        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       12.03        19.59        11.51        20.19        20.42        17.75 
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-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 
       15.58         7.53        12.39        10.13        12.43         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-A1D8 TCGA-DM-A1DB 
       24.43       130.65        92.75        49.91        12.59        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17         6.12        26.47        81.37 
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-F4-6461 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-A5IV TCGA-NH-A6GA TCGA-QG-A5YV 
       46.75        47.15        52.80         2.79         5.98        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       17.29        14.76        24.13        17.23        43.04        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       12.72        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3608 
        2.01        24.00         1.02         2.01         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3878 
       19.99        19.99         7.99        29.98        32.98         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 
       19.99        36.95        13.02        14.01        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 
       28.04         1.02         0.99        20.98        13.94        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        51.98        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 
        1.45         0.69         0.72         4.60         1.81         6.97 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
       60.03        15.02        12.00        15.02        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        0.49         2.40        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       17.69         8.61        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       37.51        14.86         0.69         0.53         1.12         0.46 
TCGA-G5-6572 
       47.08 

  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE 
                        15.915                         19.590 
[1] "0.1 - 140.4 (15.9)" "0.1 - 139.2 (19.6)"
[1] "hr=" "1"  
D57V2, continuous
D57V3, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED   138  67
  DEL PEAK 30(14Q31.1) WILD-TYPE 291  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED    138   67
  DEL PEAK 30(14Q31.1) WILD-TYPE  291   92
        clus
vv       DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  COLON                           138                            291
  RECTUM                           67                             92
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 30(14Q31.1) MUTATED        32        0        9        55         1
  DEL PEAK 30(14Q31.1) WILD-TYPE      70        1       27       110         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(14Q31.1) MUTATED           2        10         10         28
  DEL PEAK 30(14Q31.1) WILD-TYPE         1        16         12         48
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 30(14Q31.1) MUTATED           18       26        11         1
  DEL PEAK 30(14Q31.1) WILD-TYPE         34       34        14         0
D57V4, multiclass
            clus
vv           DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  STAGE I                              32                             70
  STAGE IA                              0                              1
  STAGE II                              9                             27
  STAGE IIA                            55                            110
  STAGE IIB                             1                              9
  STAGE IIC                             2                              1
  STAGE III                            10                             16
  STAGE IIIA                           10                             12
  STAGE IIIB                           28                             48
  STAGE IIIC                           18                             34
  STAGE IV                             26                             34
  STAGE IVA                            11                             14
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 30(14Q31.1) MUTATED       9  33 149  16
  DEL PEAK 30(14Q31.1) WILD-TYPE    11  72 254  46
D57V5, multiclass
       clus
vv      DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  T0+T1                            9                             11
  T2                              33                             72
  T3                             149                            254
  T4                              16                             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
  DEL PEAK 30(14Q31.1) MUTATED   106  64  37
  DEL PEAK 30(14Q31.1) WILD-TYPE 229  82  71
D57V6, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  N0                          106                            229
  N1                           64                             82
  N2                           37                             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 30(14Q31.1) MUTATED   149  35   3   1  16
  DEL PEAK 30(14Q31.1) WILD-TYPE 294  37   6   0  42
D57V7, multiclass
     clus
vv    DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  M0                           149                            294
  M1                            35                             37
  M1A                            3                              6
  M1B                            1                              0
  MX                            16                             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"
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED    91 116
  DEL PEAK 30(14Q31.1) WILD-TYPE 186 199
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED     91  116
  DEL PEAK 30(14Q31.1) WILD-TYPE  186  199
        clus
vv       DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  FEMALE                           91                            186
  MALE                            116                            199
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                    132
  DEL PEAK 30(14Q31.1) WILD-TYPE                  241
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                               5
  DEL PEAK 30(14Q31.1) WILD-TYPE                            50
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                      64
  DEL PEAK 30(14Q31.1) WILD-TYPE                    79
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(14Q31.1) MUTATED                                1
  DEL PEAK 30(14Q31.1) WILD-TYPE                             12
D57V9, multiclass
                                clus
vv                               DEL PEAK 30(14Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    132
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    64
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 30(14Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      241
  COLON MUCINOUS ADENOCARCINOMA                              50
  RECTAL ADENOCARCINOMA                                      79
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D57V10, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q31.1) MUTATED     2 205
  DEL PEAK 30(14Q31.1) WILD-TYPE   7 378
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q31.1) MUTATED      2  205
  DEL PEAK 30(14Q31.1) WILD-TYPE    7  378
     clus
vv    DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  NO                             2                              7
  YES                          205                            378
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(14Q31.1) MUTATED   142   2  15   9
  DEL PEAK 30(14Q31.1) WILD-TYPE 284   3  21  18
D57V11, multiclass
    clus
vv   DEL PEAK 30(14Q31.1) MUTATED DEL PEAK 30(14Q31.1) WILD-TYPE
  R0                          142                            284
  R1                            2                              3
  R2                           15                             21
  RX                            9                             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"
D57V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 30(14Q31.1) MUTATED                                  0     4
  DEL PEAK 30(14Q31.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(14Q31.1) MUTATED                          14   100
  DEL PEAK 30(14Q31.1) WILD-TYPE                        30   192
D57V13, multiclass
                                  clus
vv                                 DEL PEAK 30(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     100
                                  clus
vv                                 DEL PEAK 30(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    30
  WHITE                                                       192
[1] 4 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 31(14Q31.1) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(14Q31.1) MUTATED   162  35
  DEL PEAK 31(14Q31.1) WILD-TYPE 295  71
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                           197                            366 
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                            35                             71 
$`DEL PEAK 31(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-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 
       75.25         1.41         5.65        22.36        29.56         5.23 
TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-5912 
        1.94         3.06         2.14         0.07         0.26        48.20 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5868 TCGA-CM-6163 
        2.01         8.02         8.02        27.02        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-AF-2689 
       36.72        91.79         4.11         5.06         5.59        17.95 
TCGA-AF-2692 TCGA-AF-3911 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
       13.55        37.74         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3883 
       12.03         6.05         0.99         1.02         0.99         1.02 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-4005 
       17.03        35.01         1.02        48.03        36.03        14.04 
TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01W TCGA-AG-A026 
       17.03         6.02        25.97        23.01        70.03         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
       38.96        38.04         0.49        10.19         6.05         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37         4.73        13.97         7.99        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       12.99        13.97        36.00         7.10        13.05        10.06 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 
      129.27        51.48        20.55        17.00        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
       16.41        10.78        11.97        31.30         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.76        18.28        55.76        26.43 

$`DEL PEAK 31(14Q31.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
       44.91        13.94        37.05        37.25        16.04        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 
       29.19        33.53        22.09        22.06        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       27.09         8.38        25.18        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        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-3514 TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
        1.02        13.02         1.02        37.05        36.03         8.05 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01         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-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 
       61.02        78.08         6.05         6.97        54.02         0.92 
TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3710 
       47.05        11.01         5.98        36.00         5.03        26.99 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 
       19.04         0.99        35.05         0.99         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3844 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 
       15.95        38.99        14.93         0.99        33.07        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3870 
       32.05         0.99        31.07        53.00        27.02        29.98 
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-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3986 
       34.03         2.01        13.05        25.02        27.02        19.07 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        13.94        38.04        19.00        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 
       18.05        18.05         4.01         0.99        17.03        34.98 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       15.02         0.99        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-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y 
       39.98         5.03         0.92        22.03        41.00        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 
       18.05         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        0.72         0.76         0.20         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4313 TCGA-AZ-4315 
       16.31        21.44        17.82         5.19        50.37        58.39 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       32.94         5.13        83.80        65.00        62.79        61.41 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6607 
       49.41         6.77        12.10       100.01        11.74         3.19 
TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
        2.24         3.25         3.29         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        21.01         2.93       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
       37.02        26.04        13.02        29.06        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-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-6677 TCGA-CM-6678 TCGA-CM-6680 
       14.04        11.01        12.95        11.08        11.01        12.03 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 
       19.59        11.51        20.19        20.42        17.75         7.92 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        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-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64         1.51        12.00        10.26       119.70        24.43 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB 
      130.65        92.75        49.91        12.59        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28G 
        7.76       139.17         6.12        26.47        81.37        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-F4-6704 TCGA-F4-6805 TCGA-F4-6807 
       13.45         6.18        35.87         1.55        16.31        16.24 
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-G4-6317 TCGA-G4-6320 TCGA-G4-6321 
       45.11        39.42        35.93        36.00        26.43        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6626 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        46.75        47.15 
TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
       52.80         2.79         5.98        26.99        17.29        14.76 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       24.13        17.23        43.04        19.10        12.72        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50         8.45        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
        1.02         2.01         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        7.99        29.98        32.98         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 
       13.02        14.01        32.02        19.99        28.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.98        13.94        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 
        9.07         1.02        12.00        31.00        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 
       51.98        49.97        61.97        41.00         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-5337 
        0.72         4.60         1.81         6.97        60.03        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       12.00        15.02        30.05        12.95         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24        24.13        32.61         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 
       19.96        20.91        18.28        15.85        17.69         8.61 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       14.86         0.69         0.53         1.12         0.46        47.08 

  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                        16.310                         19.265 
[1] "0.1 - 140.4 (16.3)" "0.1 - 139.2 (19.3)"
[1] "hr=" "1.1"
D58V2, continuous
D58V3, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q31.1) MUTATED   140  66
  DEL PEAK 31(14Q31.1) WILD-TYPE 289  93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q31.1) MUTATED    140   66
  DEL PEAK 31(14Q31.1) WILD-TYPE  289   93
        clus
vv       DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  COLON                           140                            289
  RECTUM                           66                             93
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 31(14Q31.1) MUTATED        32        0        9        55         1
  DEL PEAK 31(14Q31.1) WILD-TYPE      70        1       27       110         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(14Q31.1) MUTATED           1        10         10         30
  DEL PEAK 31(14Q31.1) WILD-TYPE         2        16         12         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 31(14Q31.1) MUTATED           18       26        11         1
  DEL PEAK 31(14Q31.1) WILD-TYPE         34       34        14         0
D58V4, multiclass
            clus
vv           DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  STAGE I                              32                             70
  STAGE IA                              0                              1
  STAGE II                              9                             27
  STAGE IIA                            55                            110
  STAGE IIB                             1                              9
  STAGE IIC                             1                              2
  STAGE III                            10                             16
  STAGE IIIA                           10                             12
  STAGE IIIB                           30                             46
  STAGE IIIC                           18                             34
  STAGE IV                             26                             34
  STAGE IVA                            11                             14
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 31(14Q31.1) MUTATED       9  33 150  16
  DEL PEAK 31(14Q31.1) WILD-TYPE    11  72 253  46
D58V5, multiclass
       clus
vv      DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  T0+T1                            9                             11
  T2                              33                             72
  T3                             150                            253
  T4                              16                             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
  DEL PEAK 31(14Q31.1) MUTATED   105  66  37
  DEL PEAK 31(14Q31.1) WILD-TYPE 230  80  71
D58V6, multiclass
    clus
vv   DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  N0                          105                            230
  N1                           66                             80
  N2                           37                             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 31(14Q31.1) MUTATED   150  35   3   1  16
  DEL PEAK 31(14Q31.1) WILD-TYPE 293  37   6   0  42
D58V7, multiclass
     clus
vv    DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  M0                           150                            293
  M1                            35                             37
  M1A                            3                              6
  M1B                            1                              0
  MX                            16                             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"
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q31.1) MUTATED    91 117
  DEL PEAK 31(14Q31.1) WILD-TYPE 186 198
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q31.1) MUTATED     91  117
  DEL PEAK 31(14Q31.1) WILD-TYPE  186  198
        clus
vv       DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  FEMALE                           91                            186
  MALE                            117                            198
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 31(14Q31.1) MUTATED                    134
  DEL PEAK 31(14Q31.1) WILD-TYPE                  239
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(14Q31.1) MUTATED                               5
  DEL PEAK 31(14Q31.1) WILD-TYPE                            50
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 31(14Q31.1) MUTATED                      63
  DEL PEAK 31(14Q31.1) WILD-TYPE                    80
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(14Q31.1) MUTATED                                1
  DEL PEAK 31(14Q31.1) WILD-TYPE                             12
D58V9, multiclass
                                clus
vv                               DEL PEAK 31(14Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    134
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    63
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 31(14Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      239
  COLON MUCINOUS ADENOCARCINOMA                              50
  RECTAL ADENOCARCINOMA                                      80
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D58V10, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q31.1) MUTATED     2 206
  DEL PEAK 31(14Q31.1) WILD-TYPE   7 377
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q31.1) MUTATED      2  206
  DEL PEAK 31(14Q31.1) WILD-TYPE    7  377
     clus
vv    DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  NO                             2                              7
  YES                          206                            377
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(14Q31.1) MUTATED   142   2  15   9
  DEL PEAK 31(14Q31.1) WILD-TYPE 284   3  21  18
D58V11, multiclass
    clus
vv   DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  R0                          142                            284
  R1                            2                              3
  R2                           15                             21
  RX                            9                             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"
D58V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 31(14Q31.1) MUTATED                                  0     4
  DEL PEAK 31(14Q31.1) WILD-TYPE                                1     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(14Q31.1) MUTATED                          14   101
  DEL PEAK 31(14Q31.1) WILD-TYPE                        30   191
D58V13, multiclass
                                  clus
vv                                 DEL PEAK 31(14Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     101
                                  clus
vv                                 DEL PEAK 31(14Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    30
  WHITE                                                       191
[1] 4 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 32(15Q11.2) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(15Q11.2) MUTATED   184  43
  DEL PEAK 32(15Q11.2) WILD-TYPE 273  63
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                           227                            336 
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                            43                             63 
$`DEL PEAK 32(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-AZ-4681 
       14.50        16.31         0.95        15.75         5.52        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       65.00        62.79        61.41        29.56         5.23         3.19 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 
        2.14         0.26         1.35       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-D5-6531 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 
       20.19        17.75         1.32        15.12        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 
        7.53        10.13         9.04        11.38       130.65        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A285 
       13.32        12.59       140.38         7.50       131.51         6.12 
TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 
       14.04        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-G4-6294 
       16.24        33.67         1.28         0.53        35.41        28.21 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
        8.35        43.07        61.87        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50V TCGA-AF-2687 TCGA-AF-2691 
       36.00        91.79        46.75         5.06        24.13        43.04 
TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 
       13.55        37.74        14.50        10.39        32.02         1.02 
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 
        2.01        46.03        34.03         6.05        19.99        29.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 
        0.99        19.99        17.03        35.01         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       28.04        14.04        17.03        13.94        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G 
       37.02         1.02        12.00        64.01         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
       41.00        38.04         0.49         0.69        10.19         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        9.37         4.73         7.99        12.99        13.97        36.00 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       13.05        10.06        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       51.48         0.49         2.40        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       11.51        10.78        13.64        11.97        31.30        14.86 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        1.02         0.66         0.69        18.28        26.43 

$`DEL PEAK 32(15Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2682 
        5.06        37.02        46.65        23.38        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-A5ZU TCGA-AA-3492 TCGA-AA-3495 
       19.66        16.24        24.92         9.63         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        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-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-3831 
        0.99         0.99        35.05         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3844 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 
       15.95        14.93        33.07        32.05        31.07        53.00 
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-3977 
       24.00         2.01        20.98        34.03        16.08        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-A01G TCGA-AA-A01I TCGA-AA-A01P 
       21.99        34.98         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-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         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-6964 TCGA-AD-6965 TCGA-AM-5821 
       56.55         0.79         0.72         0.76         0.20         0.92 
TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
       27.09         0.20        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-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       22.36        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
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-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 
       20.02        37.02        26.04         8.02        22.03        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-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-D5-5537 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       12.95        14.99        19.59        13.51        11.51        20.42 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       18.25         7.92        17.85         4.50        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.39        12.43        14.30         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-A1D6 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A 
       49.91        44.32       135.65         7.76       139.17        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-G4-6304 
       19.43       107.67        82.39        23.51        74.56        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       44.68        51.75        39.42        35.93        26.43        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-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX 
        4.11         2.79         5.98         5.59        26.99        17.29 
TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 
       14.76        17.95        17.23        19.10        12.72        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
        8.45        15.39        20.02        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        7.07        24.00         1.02         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99         1.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       32.98         0.99         1.02        36.95        13.02        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       48.03        32.02        36.03         1.02         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W 
        6.02        15.95        36.03         9.07        31.00        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 
       10.98        51.98        49.97        61.97         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 
        4.60         1.81         6.05         6.97        13.97        60.03 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       10.98        11.01        15.02        12.00        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6506 
       30.05        12.95         5.29       126.44        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
       16.34        17.46         8.45         9.96        37.51         0.39 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 

  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                         17.79                          17.95 
[1] "0.1 - 140.4 (17.8)" "0.1 - 139.2 (17.9)"
[1] "hr=" "1"  
D59V2, continuous
D59V3, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q11.2) MUTATED   165  72
  DEL PEAK 32(15Q11.2) WILD-TYPE 264  87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q11.2) MUTATED    165   72
  DEL PEAK 32(15Q11.2) WILD-TYPE  264   87
        clus
vv       DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  COLON                           165                            264
  RECTUM                           72                             87
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 32(15Q11.2) MUTATED        38        0        9        62         3
  DEL PEAK 32(15Q11.2) WILD-TYPE      64        1       27       103         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(15Q11.2) MUTATED           2         8         12         32
  DEL PEAK 32(15Q11.2) WILD-TYPE         1        18         10         44
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 32(15Q11.2) MUTATED           26       30        12         1
  DEL PEAK 32(15Q11.2) WILD-TYPE         26       30        13         0
D59V4, multiclass
            clus
vv           DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  STAGE I                              38                             64
  STAGE IA                              0                              1
  STAGE II                              9                             27
  STAGE IIA                            62                            103
  STAGE IIB                             3                              7
  STAGE IIC                             2                              1
  STAGE III                             8                             18
  STAGE IIIA                           12                             10
  STAGE IIIB                           32                             44
  STAGE IIIC                           26                             26
  STAGE IV                             30                             30
  STAGE IVA                            12                             13
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 32(15Q11.2) MUTATED       9  39 169  23
  DEL PEAK 32(15Q11.2) WILD-TYPE    11  66 234  39
D59V5, multiclass
       clus
vv      DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  T0+T1                            9                             11
  T2                              39                             66
  T3                             169                            234
  T4                              23                             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 32(15Q11.2) MUTATED   120  70  50
  DEL PEAK 32(15Q11.2) WILD-TYPE 215  76  58
D59V6, multiclass
    clus
vv   DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  N0                          120                            215
  N1                           70                             76
  N2                           50                             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 32(15Q11.2) MUTATED   172  36   5   1  22
  DEL PEAK 32(15Q11.2) WILD-TYPE 271  36   4   0  36
D59V7, multiclass
     clus
vv    DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  M0                           172                            271
  M1                            36                             36
  M1A                            5                              4
  M1B                            1                              0
  MX                            22                             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"
D59V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q11.2) MUTATED   107 133
  DEL PEAK 32(15Q11.2) WILD-TYPE 170 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q11.2) MUTATED    107  133
  DEL PEAK 32(15Q11.2) WILD-TYPE  170  182
        clus
vv       DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  FEMALE                          107                            170
  MALE                            133                            182
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 32(15Q11.2) MUTATED                    151
  DEL PEAK 32(15Q11.2) WILD-TYPE                  222
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(15Q11.2) MUTATED                              13
  DEL PEAK 32(15Q11.2) WILD-TYPE                            42
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 32(15Q11.2) MUTATED                      65
  DEL PEAK 32(15Q11.2) WILD-TYPE                    78
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(15Q11.2) MUTATED                                6
  DEL PEAK 32(15Q11.2) WILD-TYPE                              7
D59V9, multiclass
                                clus
vv                               DEL PEAK 32(15Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    151
  COLON MUCINOUS ADENOCARCINOMA                            13
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 32(15Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      222
  COLON MUCINOUS ADENOCARCINOMA                              42
  RECTAL ADENOCARCINOMA                                      78
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q11.2) MUTATED     7 233
  DEL PEAK 32(15Q11.2) WILD-TYPE   2 350
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q11.2) MUTATED      7  233
  DEL PEAK 32(15Q11.2) WILD-TYPE    2  350
     clus
vv    DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  NO                             7                              2
  YES                          233                            350
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(15Q11.2) MUTATED   169   2  15   8
  DEL PEAK 32(15Q11.2) WILD-TYPE 257   3  21  19
D59V11, multiclass
    clus
vv   DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  R0                          169                            257
  R1                            2                              3
  R2                           15                             21
  RX                            8                             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"
D59V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 32(15Q11.2) MUTATED                                  1     3
  DEL PEAK 32(15Q11.2) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(15Q11.2) MUTATED                          13   127
  DEL PEAK 32(15Q11.2) WILD-TYPE                        31   165
D59V13, multiclass
                                  clus
vv                                 DEL PEAK 32(15Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  13
  WHITE                                                     127
                                  clus
vv                                 DEL PEAK 32(15Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    31
  WHITE                                                       165
[1] 4 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 33(15Q15.2) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(15Q15.2) MUTATED   182  42
  DEL PEAK 33(15Q15.2) WILD-TYPE 275  64
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                           224                            339 
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                            42                             64 
$`DEL PEAK 33(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-AZ-4681 
       16.31         0.95        15.75         0.20         5.52        83.80 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       65.00        62.79        61.41        29.56         5.23         3.19 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 
        2.14         0.26       102.44        48.20         2.01         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       27.02        13.02        29.06         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       14.04        29.03        16.04        15.02        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 
       11.08        11.01        10.06        12.03        12.26        20.19 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
        1.32        15.12         7.53        10.13         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       11.38       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1HA TCGA-DM-A285 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 
      131.51         6.12        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-G4-6303 TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 
       28.21         8.35        61.87        55.04        45.11        36.72 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50V TCGA-AF-2687 
       36.00        26.04        91.79        46.75         5.06        24.13 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AG-3578 
       43.04        13.55        37.74        14.50        10.39        32.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 
        1.02         2.01        24.00        46.03        34.03         6.05 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 
       19.99         0.99        29.98        32.98         0.99        19.99 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       17.03        35.01         1.02        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       17.03        13.94        25.97        23.01        37.02         1.02 
TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       12.00         1.94        38.96        41.00        38.04         0.49 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 
        0.69        10.19         6.05         9.37         4.73         7.99 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC 
       12.99        13.97        36.00        13.05        10.06        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 
       57.24        24.13        51.48         0.49         2.40        15.85 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       11.97        31.30        14.86         1.02         0.66         0.69 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`DEL PEAK 33(15Q15.2) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       46.65        23.38        35.11        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       16.04        14.53        31.63        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 
       22.06        32.71        27.09        24.13         8.38        25.18 
TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 
       24.16        24.69        24.39        23.87        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 
       24.92         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-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 
       29.00        29.00        26.01         0.99        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3681 
       54.02        14.01         0.92        47.05        15.02         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3811 TCGA-AA-3812 
        5.03        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-3844 
        0.99        25.02         1.02        17.98        15.95        14.93 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       32.05        31.07        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 
        2.01        24.00        33.01        26.01        24.00         2.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 
       20.98        34.03        16.08        26.01        25.02        19.07 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
        7.96        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z 
       18.05        17.03         4.01        27.02         0.99        21.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98         0.99        32.02        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-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         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-6964 TCGA-AD-6965 TCGA-AM-5820 
       56.55         0.79         0.72         0.76         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 
        0.92        27.09        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-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6601 TCGA-AZ-6606 
       22.36        49.41         6.77        12.10       100.01        11.74 
TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
        1.94         2.24         3.06         3.25         3.29         0.07 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10         1.35        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        21.01         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-D5-6531 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-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 
       17.13        12.49        16.14        15.58        12.39        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       14.30         9.44        11.64         1.51        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB 
      119.70        24.43        38.20        49.91         7.50        44.32 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        14.04        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 
      119.93        60.79       117.07        98.24         8.61        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 
       13.64        13.45         6.18        16.31        29.59        19.43 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
      107.67        82.39        23.51        74.56        43.07        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6320 TCGA-G4-6321 
       44.68        51.75        39.42        35.93        26.43        22.09 
TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50T 
       13.78        35.80        26.17        47.15        52.80         4.11 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 
        2.79         5.98         5.59        26.99        17.29        14.76 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       17.95        17.23        19.10        12.72        10.39         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       15.39        20.02        36.03        12.00         8.02         7.07 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
        1.02         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
       19.99         7.99         1.02         0.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 
       13.02        14.01        48.03        32.02        36.03         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        0.99        20.98         6.02        15.95        36.03         9.07 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       61.97         1.45         0.72         4.60         1.81         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        6.97        13.97        60.03        10.98        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       12.00        15.02         7.10        30.05        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      126.44       129.27        32.61        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6917 TCGA-EI-7004 
       17.00        18.28        17.69        16.34        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        9.96        37.51         0.39         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.46        55.76        47.08 

  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                         17.41                          17.95 
[1] "0.1 - 140.4 (17.4)" "0.1 - 139.2 (17.9)"
[1] "hr=" "1"  
D60V2, continuous
D60V3, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.2) MUTATED   159  75
  DEL PEAK 33(15Q15.2) WILD-TYPE 270  84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.2) MUTATED    159   75
  DEL PEAK 33(15Q15.2) WILD-TYPE  270   84
        clus
vv       DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  COLON                           159                            270
  RECTUM                           75                             84
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 33(15Q15.2) MUTATED        39        0        8        59         3
  DEL PEAK 33(15Q15.2) WILD-TYPE      63        1       28       106         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(15Q15.2) MUTATED           2         9         10         32
  DEL PEAK 33(15Q15.2) WILD-TYPE         1        17         12         44
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 33(15Q15.2) MUTATED           25       33        11         1
  DEL PEAK 33(15Q15.2) WILD-TYPE         27       27        14         0
D60V4, multiclass
            clus
vv           DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  STAGE I                              39                             63
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            59                            106
  STAGE IIB                             3                              7
  STAGE IIC                             2                              1
  STAGE III                             9                             17
  STAGE IIIA                           10                             12
  STAGE IIIB                           32                             44
  STAGE IIIC                           25                             27
  STAGE IV                             33                             27
  STAGE IVA                            11                             14
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 33(15Q15.2) MUTATED       9  39 167  22
  DEL PEAK 33(15Q15.2) WILD-TYPE    11  66 236  40
D60V5, multiclass
       clus
vv      DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  T0+T1                            9                             11
  T2                              39                             66
  T3                             167                            236
  T4                              22                             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 33(15Q15.2) MUTATED   116  73  48
  DEL PEAK 33(15Q15.2) WILD-TYPE 219  73  60
D60V6, multiclass
    clus
vv   DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  N0                          116                            219
  N1                           73                             73
  N2                           48                             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 33(15Q15.2) MUTATED   165  38   5   1  23
  DEL PEAK 33(15Q15.2) WILD-TYPE 278  34   4   0  35
D60V7, multiclass
     clus
vv    DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  M0                           165                            278
  M1                            38                             34
  M1A                            5                              4
  M1B                            1                              0
  MX                            23                             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"
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.2) MUTATED   104 133
  DEL PEAK 33(15Q15.2) WILD-TYPE 173 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.2) MUTATED    104  133
  DEL PEAK 33(15Q15.2) WILD-TYPE  173  182
        clus
vv       DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  FEMALE                          104                            173
  MALE                            133                            182
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 33(15Q15.2) MUTATED                    146
  DEL PEAK 33(15Q15.2) WILD-TYPE                  227
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q15.2) MUTATED                              12
  DEL PEAK 33(15Q15.2) WILD-TYPE                            43
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 33(15Q15.2) MUTATED                      68
  DEL PEAK 33(15Q15.2) WILD-TYPE                    75
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q15.2) MUTATED                                6
  DEL PEAK 33(15Q15.2) WILD-TYPE                              7
D60V9, multiclass
                                clus
vv                               DEL PEAK 33(15Q15.2) MUTATED
  COLON ADENOCARCINOMA                                    146
  COLON MUCINOUS ADENOCARCINOMA                            12
  RECTAL ADENOCARCINOMA                                    68
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 33(15Q15.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      227
  COLON MUCINOUS ADENOCARCINOMA                              43
  RECTAL ADENOCARCINOMA                                      75
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.2) MUTATED     7 230
  DEL PEAK 33(15Q15.2) WILD-TYPE   2 353
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.2) MUTATED      7  230
  DEL PEAK 33(15Q15.2) WILD-TYPE    2  353
     clus
vv    DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  NO                             7                              2
  YES                          230                            353
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(15Q15.2) MUTATED   169   2  16   7
  DEL PEAK 33(15Q15.2) WILD-TYPE 257   3  20  20
D60V11, multiclass
    clus
vv   DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  R0                          169                            257
  R1                            2                              3
  R2                           16                             20
  RX                            7                             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"
D60V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 33(15Q15.2) MUTATED                                  1     2
  DEL PEAK 33(15Q15.2) WILD-TYPE                                0    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(15Q15.2) MUTATED                          14   124
  DEL PEAK 33(15Q15.2) WILD-TYPE                        30   168
D60V13, multiclass
                                  clus
vv                                 DEL PEAK 33(15Q15.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     124
                                  clus
vv                                 DEL PEAK 33(15Q15.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    30
  WHITE                                                       168
[1] 4 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 34(15Q21.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(15Q21.1) MUTATED   182  39
  DEL PEAK 34(15Q21.1) WILD-TYPE 275  67
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                           221                            342 
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                            39                             67 
$`DEL PEAK 34(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-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 
       15.75         0.20         5.52        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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       16.04        15.02        13.05        11.08        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 
       10.06        12.03        12.26        20.19         1.32        15.12 
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-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 
       92.75        13.32        12.59       140.38       131.51         6.12 
TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 
       35.97        95.18        13.38        35.87         1.55        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 
       33.67         1.28         0.53        35.41         8.35        61.87 
TCGA-G4-6307 TCGA-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6625 
       55.04        45.11        36.72        36.00        26.04        91.79 
TCGA-G4-6626 TCGA-NH-A50V TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 
       46.75         5.06        24.13        43.04        13.55        37.74 
TCGA-AF-4110 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       14.50        10.39        32.02         1.02         2.01        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
       46.03        34.03         6.05        19.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
       32.98         0.99        19.99        17.03        35.01         1.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H 
       19.99        28.04        14.04        17.03        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G 
       23.01        37.02         1.02        12.00         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
       41.00        38.04         0.49         0.69        10.19         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        9.37         4.73         7.99        12.99        13.97        36.00 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       13.05        10.06        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
        0.49         2.40        15.85        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       11.51        10.78        13.64        11.97        31.30        14.86 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        1.02         0.66         0.69        18.28        26.43 

$`DEL PEAK 34(15Q21.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2684 
        5.06        46.65        42.28        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-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 
       16.24        24.92        52.44         9.63         3.02        37.05 
TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3516 
        1.02        35.01        58.03        63.98         1.02        13.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3526 
       38.99         1.02        24.03        36.03         8.05        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 
       19.07        34.03        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-A00J 
       19.07         7.96        27.02        13.94        38.04        18.05 
TCGA-AA-A00K TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00Z 
       18.05        17.03         4.01        27.02         0.99        21.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       34.98         0.99        32.02        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-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         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-6964 TCGA-AD-6965 TCGA-AM-5820 
       56.55         0.79         0.72         0.76         0.20         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31         0.95        21.44        17.82 
TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.19        75.25        50.37        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       32.94         5.13        22.36        49.41         6.77        12.10 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
      100.01        11.74         1.94         2.24         3.06         3.25 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
        3.29         0.07         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        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        2.93       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4750 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
        8.02        22.03        22.98        30.08        16.01        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        12.00        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 TCGA-D5-5539 
       13.02        14.04        11.01        12.95        14.99        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       13.51        11.51        20.42        17.75        18.25         7.92 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.39        12.43        14.30         9.44        11.64         1.51 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D6 
       12.00        10.26       119.70        24.43        38.20        49.91 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
        7.50        44.32       135.65         7.76       139.17        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-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-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       29.59        19.43       107.67        28.21        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 
       74.56        43.07        53.62        44.68        51.75        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-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       47.15        52.80         4.11         2.79         5.98         5.59 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 
       26.99        17.29        14.76        17.95        17.23        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 
       12.72        10.39         8.45        15.39        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
       12.00         8.02         7.07         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 
       12.03         0.99        15.95        19.99         7.99         1.02 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 
        0.99         1.02        36.95        13.02        14.01        48.03 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       32.02        36.03         1.02         0.99        20.98         6.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 
       10.98        51.98        49.97        61.97         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 
        4.60         1.81         6.05         6.97        13.97        60.03 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       10.98        11.01        15.02        12.00        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 
       30.05        12.95         5.29       126.44       129.27        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
       16.34        17.46         8.45         9.96        37.51         0.39 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 

  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                         18.28                          17.90 
[1] "0.1 - 140.4 (18.3)" "0.1 - 139.2 (17.9)"
[1] "hr=" "1.1"
D61V2, continuous
D61V3, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q21.1) MUTATED   158  75
  DEL PEAK 34(15Q21.1) WILD-TYPE 271  84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q21.1) MUTATED    158   75
  DEL PEAK 34(15Q21.1) WILD-TYPE  271   84
        clus
vv       DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  COLON                           158                            271
  RECTUM                           75                             84
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 34(15Q21.1) MUTATED        37        0        8        62         4
  DEL PEAK 34(15Q21.1) WILD-TYPE      65        1       28       103         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(15Q21.1) MUTATED           2         9         10         30
  DEL PEAK 34(15Q21.1) WILD-TYPE         1        17         12         46
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 34(15Q21.1) MUTATED           24       32        11         1
  DEL PEAK 34(15Q21.1) WILD-TYPE         28       28        14         0
D61V4, multiclass
            clus
vv           DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  STAGE I                              37                             65
  STAGE IA                              0                              1
  STAGE II                              8                             28
  STAGE IIA                            62                            103
  STAGE IIB                             4                              6
  STAGE IIC                             2                              1
  STAGE III                             9                             17
  STAGE IIIA                           10                             12
  STAGE IIIB                           30                             46
  STAGE IIIC                           24                             28
  STAGE IV                             32                             28
  STAGE IVA                            11                             14
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 34(15Q21.1) MUTATED       8  38 166  23
  DEL PEAK 34(15Q21.1) WILD-TYPE    12  67 237  39
D61V5, multiclass
       clus
vv      DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  T0+T1                            8                             12
  T2                              38                             67
  T3                             166                            237
  T4                              23                             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 34(15Q21.1) MUTATED   118  70  47
  DEL PEAK 34(15Q21.1) WILD-TYPE 217  76  61
D61V6, multiclass
    clus
vv   DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  N0                          118                            217
  N1                           70                             76
  N2                           47                             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 34(15Q21.1) MUTATED   165  37   5   1  23
  DEL PEAK 34(15Q21.1) WILD-TYPE 278  35   4   0  35
D61V7, multiclass
     clus
vv    DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  M0                           165                            278
  M1                            37                             35
  M1A                            5                              4
  M1B                            1                              0
  MX                            23                             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"
D61V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q21.1) MUTATED   102 133
  DEL PEAK 34(15Q21.1) WILD-TYPE 175 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q21.1) MUTATED    102  133
  DEL PEAK 34(15Q21.1) WILD-TYPE  175  182
        clus
vv       DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  FEMALE                          102                            175
  MALE                            133                            182
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 34(15Q21.1) MUTATED                    145
  DEL PEAK 34(15Q21.1) WILD-TYPE                  228
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(15Q21.1) MUTATED                              12
  DEL PEAK 34(15Q21.1) WILD-TYPE                            43
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 34(15Q21.1) MUTATED                      68
  DEL PEAK 34(15Q21.1) WILD-TYPE                    75
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(15Q21.1) MUTATED                                6
  DEL PEAK 34(15Q21.1) WILD-TYPE                              7
D61V9, multiclass
                                clus
vv                               DEL PEAK 34(15Q21.1) MUTATED
  COLON ADENOCARCINOMA                                    145
  COLON MUCINOUS ADENOCARCINOMA                            12
  RECTAL ADENOCARCINOMA                                    68
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 34(15Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      228
  COLON MUCINOUS ADENOCARCINOMA                              43
  RECTAL ADENOCARCINOMA                                      75
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q21.1) MUTATED     7 228
  DEL PEAK 34(15Q21.1) WILD-TYPE   2 355
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q21.1) MUTATED      7  228
  DEL PEAK 34(15Q21.1) WILD-TYPE    2  355
     clus
vv    DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  NO                             7                              2
  YES                          228                            355
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(15Q21.1) MUTATED   168   1  16   7
  DEL PEAK 34(15Q21.1) WILD-TYPE 258   4  20  20
D61V11, multiclass
    clus
vv   DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  R0                          168                            258
  R1                            1                              4
  R2                           16                             20
  RX                            7                             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"
D61V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 34(15Q21.1) MUTATED                                  1     2
  DEL PEAK 34(15Q21.1) WILD-TYPE                                0    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(15Q21.1) MUTATED                          11   122
  DEL PEAK 34(15Q21.1) WILD-TYPE                        33   170
D61V13, multiclass
                                  clus
vv                                 DEL PEAK 34(15Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  11
  WHITE                                                     122
                                  clus
vv                                 DEL PEAK 34(15Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    33
  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(62) Variable = DEL PEAK 35(15Q22.33) MUTATION ANALYSIS
D62V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 35(15Q22.33) MUTATED   175  39
  DEL PEAK 35(15Q22.33) WILD-TYPE 282  67
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                            214                             349 
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                             39                              67 
$`DEL PEAK 35(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-AZ-4681 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        0.20         5.52        83.80        65.00        62.79        61.41 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 
       29.56         5.23         3.19         2.14         0.26       102.44 
TCGA-CK-5912 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
       48.20         2.01         8.02        27.02        13.02        29.06 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 
        5.03        15.02        17.03        14.04        29.03        16.04 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       15.02        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       20.19         1.32        15.12        17.13        12.49         7.53 
TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.13         9.04        13.41        11.38       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A285 
       49.91        13.32        12.59       140.38       131.51         6.12 
TCGA-DM-A288 TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 
       14.04        95.18        13.38        35.87         1.55        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 
       33.67         1.28         0.53        35.41         8.35        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-NH-A50V TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 
        5.06        24.13        43.04        13.55        12.72        37.74 
TCGA-AF-4110 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       14.50        10.39        32.02         1.02         2.01        24.00 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 
       34.03         6.05        15.95        19.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 
       19.99        17.03        35.01         1.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       14.04        17.03        13.94        25.97        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02        12.00        70.03        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 
        0.49         0.69        10.19         6.05         9.37         7.99 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
       10.98        12.99        13.97        36.00        13.05        10.06 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.36        57.24       129.27        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        2.40        15.85        16.31        16.41        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       13.64        11.97        31.30        14.86         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.69         0.46        18.28        26.43 

$`DEL PEAK 35(15Q22.33) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2682 
        5.06        46.65        23.38        42.28        35.11        13.94 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4105 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        16.04        14.53        32.91        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-A6-6780 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-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3506 
        9.63         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-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-3538 TCGA-AA-3543 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 
       26.01         0.99        14.01        24.00        17.95        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3663 
       20.98        13.94        61.02        78.08         6.05         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01         0.92        47.05        47.01        15.02 
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-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-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3860 
       15.95        14.93        33.07        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       53.00        27.02        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-3971 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3989 TCGA-AA-3994 
       16.08        26.01        25.02        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-A00Z TCGA-AA-A010 TCGA-AA-A01D 
        4.01        27.02         0.99        21.99        34.98         0.99 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 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-A01V TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
        1.02        35.01        37.02        39.06        51.98        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-6890 
       40.96         0.07        21.37         4.21        56.55         0.79 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
        0.72         0.76         0.20         0.92        27.09        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 
       21.01         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-CM-6675 
       12.99        13.02        14.04        11.01        12.95        13.05 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       14.99        12.26        19.59        13.51        11.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       17.75        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-D5-6930 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-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A 
        7.50        44.32       135.65         7.76       139.17        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-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-G4-6294 TCGA-G4-6297 TCGA-G4-6298 
       29.59        19.43       107.67        28.21        82.39        23.51 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 
       74.56        43.07        53.62        44.68        51.75        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-G4-6627 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-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2689 TCGA-AF-2690 
        5.59        26.99        17.29        14.76        17.95        17.23 
TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 
       19.10        10.39         8.45        15.39        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
       12.00         8.02         7.07         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       50.04        12.03         0.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        1.02        32.98         0.99         1.02        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 
       14.01        48.03        32.02        36.03         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N 
       20.98         6.02        15.95        36.03         9.07        31.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
       64.01        10.98        51.98        49.97         1.94        61.97 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        1.45         0.72         4.60         1.81         6.05         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
        4.73        13.97        60.03        11.01        15.02        12.00 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       15.02         7.10        30.05        12.95         5.29       126.44 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       17.69        16.34         8.61        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 
       37.51         0.39         0.53         1.12         0.76        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                          17.03                           18.05 
[1] "0.1 - 140.4 (17.0)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.1"
D62V2, continuous
D62V3, binary
                                 cls
clus                                0   1
  DEL PEAK 35(15Q22.33) MUTATED   148  74
  DEL PEAK 35(15Q22.33) WILD-TYPE 281  85
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(15Q22.33) MUTATED    148   74
  DEL PEAK 35(15Q22.33) WILD-TYPE  281   85
        clus
vv       DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  COLON                            148                             281
  RECTUM                            74                              85
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 35(15Q22.33) MUTATED        31        0        7        60         3
  DEL PEAK 35(15Q22.33) WILD-TYPE      71        1       29       105         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(15Q22.33) MUTATED           2         7         11         29
  DEL PEAK 35(15Q22.33) WILD-TYPE         1        19         11         47
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 35(15Q22.33) MUTATED           27       31        12         0
  DEL PEAK 35(15Q22.33) WILD-TYPE         25       29        13         1
D62V4, multiclass
            clus
vv           DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  STAGE I                               31                              71
  STAGE IA                               0                               1
  STAGE II                               7                              29
  STAGE IIA                             60                             105
  STAGE IIB                              3                               7
  STAGE IIC                              2                               1
  STAGE III                              7                              19
  STAGE IIIA                            11                              11
  STAGE IIIB                            29                              47
  STAGE IIIC                            27                              25
  STAGE IV                              31                              29
  STAGE IVA                             12                              13
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  DEL PEAK 35(15Q22.33) MUTATED       9  30 166  20
  DEL PEAK 35(15Q22.33) WILD-TYPE    11  75 237  42
D62V5, multiclass
       clus
vv      DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  T0+T1                             9                              11
  T2                               30                              75
  T3                              166                             237
  T4                               20                              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 35(15Q22.33) MUTATED   109  66  50
  DEL PEAK 35(15Q22.33) WILD-TYPE 226  80  58
D62V6, multiclass
    clus
vv   DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  N0                           109                             226
  N1                            66                              80
  N2                            50                              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 35(15Q22.33) MUTATED   157  37   5   0  21
  DEL PEAK 35(15Q22.33) WILD-TYPE 286  35   4   1  37
D62V7, multiclass
     clus
vv    DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  M0                            157                             286
  M1                             37                              35
  M1A                             5                               4
  M1B                             0                               1
  MX                             21                              37
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V8, binary
                                 cls
clus                                0   1
  DEL PEAK 35(15Q22.33) MUTATED   101 124
  DEL PEAK 35(15Q22.33) WILD-TYPE 176 191
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(15Q22.33) MUTATED    101  124
  DEL PEAK 35(15Q22.33) WILD-TYPE  176  191
        clus
vv       DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  FEMALE                           101                             176
  MALE                             124                             191
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 35(15Q22.33) MUTATED                    136
  DEL PEAK 35(15Q22.33) WILD-TYPE                  237
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(15Q22.33) MUTATED                              11
  DEL PEAK 35(15Q22.33) WILD-TYPE                            44
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 35(15Q22.33) MUTATED                      67
  DEL PEAK 35(15Q22.33) WILD-TYPE                    76
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(15Q22.33) MUTATED                                6
  DEL PEAK 35(15Q22.33) WILD-TYPE                              7
D62V9, multiclass
                                clus
vv                               DEL PEAK 35(15Q22.33) MUTATED
  COLON ADENOCARCINOMA                                     136
  COLON MUCINOUS ADENOCARCINOMA                             11
  RECTAL ADENOCARCINOMA                                     67
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 35(15Q22.33) WILD-TYPE
  COLON ADENOCARCINOMA                                       237
  COLON MUCINOUS ADENOCARCINOMA                               44
  RECTAL ADENOCARCINOMA                                       76
  RECTAL MUCINOUS ADENOCARCINOMA                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, binary
                                 cls
clus                                0   1
  DEL PEAK 35(15Q22.33) MUTATED     8 217
  DEL PEAK 35(15Q22.33) WILD-TYPE   1 366
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(15Q22.33) MUTATED      8  217
  DEL PEAK 35(15Q22.33) WILD-TYPE    1  366
     clus
vv    DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  NO                              8                               1
  YES                           217                             366
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 35(15Q22.33) MUTATED   160   1  15   7
  DEL PEAK 35(15Q22.33) WILD-TYPE 266   4  21  20
D62V11, multiclass
    clus
vv   DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  R0                           160                             266
  R1                             1                               4
  R2                            15                              21
  RX                             7                              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"
D62V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 35(15Q22.33) MUTATED                                  1     2
  DEL PEAK 35(15Q22.33) WILD-TYPE                                0    10
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(15Q22.33) MUTATED                          11   124
  DEL PEAK 35(15Q22.33) WILD-TYPE                        33   168
D62V13, multiclass
                                  clus
vv                                 DEL PEAK 35(15Q22.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   11
  WHITE                                                      124
                                  clus
vv                                 DEL PEAK 35(15Q22.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                         10
  BLACK OR AFRICAN AMERICAN                                     33
  WHITE                                                        168
[1] 4 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 36(16P13.3) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(16P13.3) MUTATED    42  19
  DEL PEAK 36(16P13.3) WILD-TYPE 415  87
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            61                            502 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            19                             87 
$`DEL PEAK 36(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-QG-A5YV TCGA-AG-3578 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 
        4.11        26.99        32.02         6.05        19.99         7.99 
TCGA-AG-4005 TCGA-AG-A02G TCGA-DC-6682 TCGA-EI-6882 TCGA-F5-6811 TCGA-F5-6814 
       14.04        38.96        13.05         8.61         1.02         0.53 
TCGA-G5-6233 
       18.28 

$`DEL PEAK 36(16P13.3) 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-A6-2678 TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        35.11        13.94        15.52        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.04        36.53        32.45        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-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.18        24.16        20.61        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B 
       20.12        19.66        20.28        16.24        24.92        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-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-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-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-3842 
        0.99        25.02         1.02        17.98        15.95        37.02 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        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-3875 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3949 
       29.98        18.05        31.00        12.99        24.00        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
       24.00        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3977 TCGA-AA-3979 TCGA-AA-3986 
       13.05        34.06        26.01        25.02        24.00        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-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-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-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-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        41.00        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-6901 TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
        1.02         0.10         0.76         0.20         0.92        27.09 
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-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-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-6715 
        2.24         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-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 
       21.01         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-5341 
       37.02         8.02        26.04         8.02        27.02        29.06 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 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-6166 TCGA-CM-6167 TCGA-CM-6168 
       12.00        14.04        29.03        21.99        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       15.02        14.04        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-D5-6535 
       11.51        20.42        18.25         1.32         7.92        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.50        17.13        12.49        16.14        15.58 
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-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 
        9.44        11.64        13.41         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-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       13.32       140.38         7.50       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-F4-6460 
       35.97        60.79       117.07        98.24        95.18        13.38 
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-F4-6806 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-G4-6295 TCGA-G4-6297 TCGA-G4-6298 
       35.41        19.43       107.67         8.35        82.39        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-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       51.75        45.11        39.42        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-G4-6625 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       91.79        47.15        52.80         5.06         2.79         5.98 
TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        5.59        17.29        14.76        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50         8.45        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        19.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        36.03         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
       14.86         0.39         0.66         0.69         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                         61.84                         140.38 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                        16.310                         18.015 
[1] "0.2 - 61.8 (16.3)"  "0.1 - 140.4 (18.0)"
[1] "hr=" "2.2"
D63V2, continuous
D63V3, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P13.3) MUTATED    52  13
  DEL PEAK 36(16P13.3) WILD-TYPE 377 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED     52   13
  DEL PEAK 36(16P13.3) WILD-TYPE  377  146
        clus
vv       DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  COLON                            52                            377
  RECTUM                           13                            146
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 36(16P13.3) MUTATED         4        0        3        23         2
  DEL PEAK 36(16P13.3) WILD-TYPE      98        1       33       142         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(16P13.3) MUTATED           1         0          0          8
  DEL PEAK 36(16P13.3) WILD-TYPE         2        26         22         68
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 36(16P13.3) MUTATED           11        8         4         0
  DEL PEAK 36(16P13.3) WILD-TYPE         41       52        21         1
D63V4, multiclass
            clus
vv           DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  STAGE I                               4                             98
  STAGE IA                              0                              1
  STAGE II                              3                             33
  STAGE IIA                            23                            142
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             0                             26
  STAGE IIIA                            0                             22
  STAGE IIIB                            8                             68
  STAGE IIIC                           11                             41
  STAGE IV                              8                             52
  STAGE IVA                             4                             21
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 36(16P13.3) MUTATED       0   6  53   6
  DEL PEAK 36(16P13.3) WILD-TYPE    20  99 350  56
D63V5, multiclass
       clus
vv      DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  T0+T1                            0                             20
  T2                               6                             99
  T3                              53                            350
  T4                               6                             56
[1] 4 2
[1] TRUE
[1] "dimension 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(16P13.3) MUTATED    32  16  17
  DEL PEAK 36(16P13.3) WILD-TYPE 303 130  91
D63V6, multiclass
    clus
vv   DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  N0                           32                            303
  N1                           16                            130
  N2                           17                             91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 36(16P13.3) MUTATED    45  10   2   0   5
  DEL PEAK 36(16P13.3) WILD-TYPE 398  62   7   1  53
D63V7, multiclass
     clus
vv    DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  M0                            45                            398
  M1                            10                             62
  M1A                            2                              7
  M1B                            0                              1
  MX                             5                             53
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P13.3) MUTATED    30  35
  DEL PEAK 36(16P13.3) WILD-TYPE 247 280
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED     30   35
  DEL PEAK 36(16P13.3) WILD-TYPE  247  280
        clus
vv       DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  FEMALE                           30                            247
  MALE                             35                            280
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 36(16P13.3) MUTATED                     46
  DEL PEAK 36(16P13.3) WILD-TYPE                  327
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(16P13.3) MUTATED                               6
  DEL PEAK 36(16P13.3) WILD-TYPE                            49
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 36(16P13.3) MUTATED                      10
  DEL PEAK 36(16P13.3) WILD-TYPE                   133
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(16P13.3) MUTATED                                2
  DEL PEAK 36(16P13.3) WILD-TYPE                             11
D63V9, multiclass
                                clus
vv                               DEL PEAK 36(16P13.3) MUTATED
  COLON ADENOCARCINOMA                                     46
  COLON MUCINOUS ADENOCARCINOMA                             6
  RECTAL ADENOCARCINOMA                                    10
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 36(16P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      327
  COLON MUCINOUS ADENOCARCINOMA                              49
  RECTAL ADENOCARCINOMA                                     133
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D63V10, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P13.3) MUTATED     0  65
  DEL PEAK 36(16P13.3) WILD-TYPE   9 518
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED      0   65
  DEL PEAK 36(16P13.3) WILD-TYPE    9  518
     clus
vv    DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  NO                             0                              9
  YES                           65                            518
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(16P13.3) MUTATED    48   1   4   1
  DEL PEAK 36(16P13.3) WILD-TYPE 378   4  32  26
D63V11, multiclass
    clus
vv   DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  R0                           48                            378
  R1                            1                              4
  R2                            4                             32
  RX                            1                             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"
D63V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 36(16P13.3) MUTATED                                  0     0
  DEL PEAK 36(16P13.3) WILD-TYPE                                1    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(16P13.3) MUTATED                           8    32
  DEL PEAK 36(16P13.3) WILD-TYPE                        36   260
D63V13, multiclass
                                  clus
vv                                 DEL PEAK 36(16P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                      32
                                  clus
vv                                 DEL PEAK 36(16P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    36
  WHITE                                                       260
[1] 4 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 37(16Q23.1) MUTATION ANALYSIS
D64V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(16Q23.1) MUTATED    57  18
  DEL PEAK 37(16Q23.1) WILD-TYPE 400  88
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            75                            488 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            18                             88 
$`DEL PEAK 37(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-QG-A5Z2 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3609 
       14.76        10.39        32.02         1.02         6.05        19.99 
TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-4005 TCGA-AH-6544 TCGA-AH-6644 
        7.99        32.98         1.02        14.04         0.49         0.72 
TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6883 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       13.05       129.27        11.51        11.97         8.45         9.96 
TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
        1.02         0.53        18.28 

$`DEL PEAK 37(16Q23.1) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2677 TCGA-A6-2679 
        5.06        46.65        43.76        43.43        17.79        44.91 
TCGA-A6-2680 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       35.11        13.94        15.52        37.05        37.25        16.04 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        36.53        14.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        23.61        22.09        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-A6-6652 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 
       24.69        23.87        20.12        19.66        20.28        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-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-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         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-3538 
       19.07        19.07        34.03        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
       12.99        14.01        33.99        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-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-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
       14.01        50.04        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 
        5.98        19.00        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-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
        1.02        15.95        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
        0.99        33.07        32.05         0.99        31.07        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-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 
       12.99        24.00        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-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-A00F TCGA-AA-A00K TCGA-AA-A00L 
       13.94        38.04        19.00        34.03        18.05        17.03 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
        4.01        27.02        42.02         0.99        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       21.99        34.98        15.02        15.02         0.99        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       12.00        31.00        31.00        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02F 
       35.01        26.01        37.02        39.06        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        2.01         5.03         0.92        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-AM-5820 
        1.58         1.02         0.10         0.76         0.20         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        15.75 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4308 TCGA-AZ-4313 
        0.20        21.44        17.82         5.19        75.25        50.37 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41        32.94        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        61.41         6.77       100.01        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         1.94         3.06         2.14         3.25         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 
       21.01         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-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 
       29.06        22.98        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-6165 
       17.03        15.02        12.00        14.04        29.03        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-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-D5-6530 
       14.99        12.26        19.59        13.51        11.51        20.42 
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-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
        1.51        12.00        11.38        10.26       119.70        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-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-G4-6297 TCGA-G4-6298 
       19.43       107.67        28.21         8.35        82.39        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-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6315 TCGA-G4-6317 
       51.75        45.11        39.42        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-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV 
       91.79        46.75        47.15        52.80         5.06         2.79 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 
        5.98         5.59        26.99        17.29        24.13        17.95 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 
       10.39        14.50         8.45        15.39        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         8.02         7.07         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       46.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       15.95        19.99         0.99        29.98         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.04         1.45         0.69         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       17.69        16.34        16.31        16.41         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       13.64        17.46        37.51        31.30        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.66         0.69         1.12         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                          0.43                           0.07 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                        129.27                         140.38 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                         14.76                          18.15 
[1] "0.4 - 129.3 (14.8)" "0.1 - 140.4 (18.1)"
[1] "hr=" "1.9"
D64V2, continuous
D64V3, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    56  23
  DEL PEAK 37(16Q23.1) WILD-TYPE 373 136
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     56   23
  DEL PEAK 37(16Q23.1) WILD-TYPE  373  136
        clus
vv       DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  COLON                            56                            373
  RECTUM                           23                            136
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 37(16Q23.1) MUTATED        13        0        5        24         2
  DEL PEAK 37(16Q23.1) WILD-TYPE      89        1       31       141         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(16Q23.1) MUTATED           2         4          0          7
  DEL PEAK 37(16Q23.1) WILD-TYPE         1        22         22         69
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 37(16Q23.1) MUTATED            6       10         4         0
  DEL PEAK 37(16Q23.1) WILD-TYPE         46       50        21         1
D64V4, multiclass
            clus
vv           DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  STAGE I                              13                             89
  STAGE IA                              0                              1
  STAGE II                              5                             31
  STAGE IIA                            24                            141
  STAGE IIB                             2                              8
  STAGE IIC                             2                              1
  STAGE III                             4                             22
  STAGE IIIA                            0                             22
  STAGE IIIB                            7                             69
  STAGE IIIC                            6                             46
  STAGE IV                             10                             50
  STAGE IVA                             4                             21
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 37(16Q23.1) MUTATED       0  14  54  11
  DEL PEAK 37(16Q23.1) WILD-TYPE    20  91 349  51
D64V5, multiclass
       clus
vv      DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  T0+T1                            0                             20
  T2                              14                             91
  T3                              54                            349
  T4                              11                             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 37(16Q23.1) MUTATED    46  16  16
  DEL PEAK 37(16Q23.1) WILD-TYPE 289 130  92
D64V6, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  N0                           46                            289
  N1                           16                            130
  N2                           16                             92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 37(16Q23.1) MUTATED    57  11   2   0   9
  DEL PEAK 37(16Q23.1) WILD-TYPE 386  61   7   1  49
D64V7, multiclass
     clus
vv    DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  M0                            57                            386
  M1                            11                             61
  M1A                            2                              7
  M1B                            0                              1
  MX                             9                             49
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    42  37
  DEL PEAK 37(16Q23.1) WILD-TYPE 235 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     42   37
  DEL PEAK 37(16Q23.1) WILD-TYPE  235  278
        clus
vv       DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  FEMALE                           42                            235
  MALE                             37                            278
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                     47
  DEL PEAK 37(16Q23.1) WILD-TYPE                  326
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                               9
  DEL PEAK 37(16Q23.1) WILD-TYPE                            46
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                      20
  DEL PEAK 37(16Q23.1) WILD-TYPE                   123
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                                2
  DEL PEAK 37(16Q23.1) WILD-TYPE                             11
D64V9, multiclass
                                clus
vv                               DEL PEAK 37(16Q23.1) MUTATED
  COLON ADENOCARCINOMA                                     47
  COLON MUCINOUS ADENOCARCINOMA                             9
  RECTAL ADENOCARCINOMA                                    20
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 37(16Q23.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      326
  COLON MUCINOUS ADENOCARCINOMA                              46
  RECTAL ADENOCARCINOMA                                     123
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D64V10, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED     1  78
  DEL PEAK 37(16Q23.1) WILD-TYPE   8 505
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      1   78
  DEL PEAK 37(16Q23.1) WILD-TYPE    8  505
     clus
vv    DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  NO                             1                              8
  YES                           78                            505
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(16Q23.1) MUTATED    54   0   3   4
  DEL PEAK 37(16Q23.1) WILD-TYPE 372   5  33  23
D64V11, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  R0                           54                            372
  R1                            0                              5
  R2                            3                             33
  RX                            4                             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"
D64V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 37(16Q23.1) MUTATED                                  0     2
  DEL PEAK 37(16Q23.1) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(16Q23.1) MUTATED                           9    34
  DEL PEAK 37(16Q23.1) WILD-TYPE                        35   258
D64V13, multiclass
                                  clus
vv                                 DEL PEAK 37(16Q23.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 37(16Q23.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    35
  WHITE                                                       258
[1] 4 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 38(17P12) MUTATION ANALYSIS
D65V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 38(17P12) MUTATED   272  64
  DEL PEAK 38(17P12) WILD-TYPE 185  42
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                         336                          227 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          64                           42 
$`DEL PEAK 38(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-A50V 
       36.72        36.00        26.43        91.79        46.75         5.06 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2689 TCGA-AF-2690 
        5.98         5.59        26.99        17.29        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        19.10        12.72        37.74        14.50 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       15.39        20.02        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        1.02        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       50.04         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 
        1.02        32.98         0.99         1.02        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       23.01        37.02        15.95         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 
       70.03        64.01        51.98         1.94        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 
        0.49         0.69         0.72         4.60        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        6.05         6.97        13.97         7.99        10.98        11.01 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       13.97        15.02         7.10        30.05        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       51.48         0.49         2.40        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31        16.41        11.51        10.78 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.39         0.69         0.53         0.76         0.46        55.76 

$`DEL PEAK 38(17P12) WILD-TYPE`
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2682 TCGA-A6-2686 TCGA-A6-3810 
       46.65        23.38        44.91        13.94        16.04        36.53 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 
       33.53        23.61        22.09        22.06         8.38        25.08 
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-A56B TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3506 TCGA-AA-3510 
       52.44         9.63         3.02        35.01        58.03        63.98 
TCGA-AA-3516 TCGA-AA-3518 TCGA-AA-3525 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       13.02         1.02         8.05        19.07        19.07        34.03 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 
       29.00        26.01         0.99        17.95        29.95        20.98 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
        6.97        54.02         0.92        47.05        15.02        11.01 
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-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-3860 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       31.07        53.00        31.00        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3986 TCGA-AA-3994 
       24.00         2.01        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-A00N 
       13.94        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        34.98        15.02        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 TCGA-AA-A02O 
       35.01        35.01        26.01        39.06        51.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6895 
       22.03        39.98        18.05         0.07        56.55         0.72 
TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.76         0.92        27.09        21.44        17.82         5.19 
TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 
       50.37        58.39        32.94        62.79        49.41         6.77 
TCGA-AZ-6601 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
      100.01        11.74         3.06         3.25         0.33         0.10 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       17.56        40.34        70.16        15.62        51.32        21.01 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
        2.93       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6162 
       22.98        30.08        16.01        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 
       14.04        16.04        12.99        14.04        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6536 TCGA-D5-6537 
       11.01        12.03        20.19        20.42        17.85         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-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 
       10.26       119.70        49.91         7.50       135.65         7.76 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6463 
       81.37        60.79        98.24        95.18         8.61        13.64 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6854 
       13.45         6.18        35.87         1.55        29.59         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6299 
       35.41        19.43       107.67        28.21        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 
       43.07        53.62        51.75        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-QG-A5Z2 TCGA-AF-2687 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3580 
       14.76        24.13        10.39         8.45        10.39         8.02 
TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3878 
        2.01        12.03         6.05        19.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4022 TCGA-AG-A002 
       19.99        36.95        13.02        14.01         0.99        20.98 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       36.03         9.07        10.98        49.97        38.96        61.97 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-5337 
        1.45         1.81         9.37         4.73        60.03        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6681 TCGA-DY-A1H8 TCGA-EI-6506 
       12.99        12.00        36.00        12.95        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 
       19.96        15.85         8.61        13.64        17.46         1.02 
TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        0.66         1.12        18.28        47.08        26.43 

  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                        0.07                         0.07 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                      140.38                       135.65 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                       17.03                        19.07 
[1] "0.1 - 140.4 (17.0)" "0.1 - 135.7 (19.1)"
[1] "hr=" "1.1"
D65V2, continuous
D65V3, binary
                              cls
clus                             0   1
  DEL PEAK 38(17P12) MUTATED   238 111
  DEL PEAK 38(17P12) WILD-TYPE 191  48
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED    238  111
  DEL PEAK 38(17P12) WILD-TYPE  191   48
        clus
vv       DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  COLON                         238                          191
  RECTUM                        111                           48
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 38(17P12) MUTATED        52        0       19        83         3
  DEL PEAK 38(17P12) WILD-TYPE      50        1       17        82         7
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(17P12) MUTATED           2        16         17         49
  DEL PEAK 38(17P12) WILD-TYPE         1        10          5         27
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 38(17P12) MUTATED           40       44        19         1
  DEL PEAK 38(17P12) WILD-TYPE         12       16         6         0
D65V4, multiclass
            clus
vv           DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  STAGE I                            52                           50
  STAGE IA                            0                            1
  STAGE II                           19                           17
  STAGE IIA                          83                           82
  STAGE IIB                           3                            7
  STAGE IIC                           2                            1
  STAGE III                          16                           10
  STAGE IIIA                         17                            5
  STAGE IIIB                         49                           27
  STAGE IIIC                         40                           12
  STAGE IV                           44                           16
  STAGE IVA                          19                            6
  STAGE IVB                           1                            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                           T0+T1  T2  T3  T4
  DEL PEAK 38(17P12) MUTATED       9  60 246  38
  DEL PEAK 38(17P12) WILD-TYPE    11  45 157  24
D65V5, multiclass
       clus
vv      DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  T0+T1                          9                           11
  T2                            60                           45
  T3                           246                          157
  T4                            38                           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
  DEL PEAK 38(17P12) MUTATED   174  99  78
  DEL PEAK 38(17P12) WILD-TYPE 161  47  30
D65V6, multiclass
    clus
vv   DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  N0                        174                          161
  N1                         99                           47
  N2                         78                           30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A M1B  MX
  DEL PEAK 38(17P12) MUTATED   255  55   6   1  32
  DEL PEAK 38(17P12) WILD-TYPE 188  17   3   0  26
D65V7, multiclass
     clus
vv    DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  M0                         255                          188
  M1                          55                           17
  M1A                          6                            3
  M1B                          1                            0
  MX                          32                           26
[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"
D65V8, binary
                              cls
clus                             0   1
  DEL PEAK 38(17P12) MUTATED   161 192
  DEL PEAK 38(17P12) WILD-TYPE 116 123
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED    161  192
  DEL PEAK 38(17P12) WILD-TYPE  116  123
        clus
vv       DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  FEMALE                        161                          116
  MALE                          192                          123
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  DEL PEAK 38(17P12) MUTATED                    223
  DEL PEAK 38(17P12) WILD-TYPE                  150
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(17P12) MUTATED                              14
  DEL PEAK 38(17P12) WILD-TYPE                            41
                              vv
clus                           RECTAL ADENOCARCINOMA
  DEL PEAK 38(17P12) MUTATED                     103
  DEL PEAK 38(17P12) WILD-TYPE                    40
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(17P12) MUTATED                                6
  DEL PEAK 38(17P12) WILD-TYPE                              7
D65V9, multiclass
                                clus
vv                               DEL PEAK 38(17P12) MUTATED
  COLON ADENOCARCINOMA                                  223
  COLON MUCINOUS ADENOCARCINOMA                          14
  RECTAL ADENOCARCINOMA                                 103
  RECTAL MUCINOUS ADENOCARCINOMA                          6
                                clus
vv                               DEL PEAK 38(17P12) WILD-TYPE
  COLON ADENOCARCINOMA                                    150
  COLON MUCINOUS ADENOCARCINOMA                            41
  RECTAL ADENOCARCINOMA                                    40
  RECTAL MUCINOUS ADENOCARCINOMA                            7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, binary
                              cls
clus                             0   1
  DEL PEAK 38(17P12) MUTATED     7 346
  DEL PEAK 38(17P12) WILD-TYPE   2 237
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED      7  346
  DEL PEAK 38(17P12) WILD-TYPE    2  237
     clus
vv    DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  NO                           7                            2
  YES                        346                          237
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 38(17P12) MUTATED   249   3  26  12
  DEL PEAK 38(17P12) WILD-TYPE 177   2  10  15
D65V11, multiclass
    clus
vv   DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  R0                        249                          177
  R1                          3                            2
  R2                         26                           10
  RX                         12                           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"
D65V12, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 38(17P12) MUTATED                                  0     7
  DEL PEAK 38(17P12) WILD-TYPE                                1     5
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(17P12) MUTATED                          23   176
  DEL PEAK 38(17P12) WILD-TYPE                        21   116
D65V13, multiclass
                                  clus
vv                                 DEL PEAK 38(17P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     7
  BLACK OR AFRICAN AMERICAN                                23
  WHITE                                                   176
                                  clus
vv                                 DEL PEAK 38(17P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       5
  BLACK OR AFRICAN AMERICAN                                  21
  WHITE                                                     116
[1] 4 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 39(17Q24.3) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(17Q24.3) MUTATED    67  19
  DEL PEAK 39(17Q24.3) WILD-TYPE 390  87
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                            86                            477 
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                            19                             87 
$`DEL PEAK 39(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-A01Z 
       34.03        42.02         0.99        32.02        33.04        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-6196 
        2.96        39.98         1.58         1.02         0.20         0.20 
TCGA-AY-A69D TCGA-AZ-6600 TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5912 TCGA-CM-4751 
        5.52        12.10         3.29         0.26        48.20        27.02 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6170 TCGA-D5-5537 TCGA-D5-6534 TCGA-D5-6539 
        5.03        15.02        15.02        14.99         7.92        12.49 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       13.41        11.38        38.20        12.59       140.38        44.32 
TCGA-DM-A280 TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6809 
        7.76       117.07        13.38        13.45         1.55         1.28 
TCGA-G4-6295 TCGA-NH-A6GA TCGA-QG-A5YV TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3581 
        8.35         5.98        26.99        14.50        15.39         7.07 
TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-A008 
        1.02         1.02         1.02        32.02        28.04        13.94 
TCGA-AG-A00H TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 
       25.97         9.07        12.00        41.00         0.69        10.19 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6508 
       13.97        15.02         7.10         5.29        24.13        20.91 
TCGA-EI-6881 TCGA-F5-6814 
       16.41         0.53 

$`DEL PEAK 39(17Q24.3) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2678 
        5.06        46.65        43.43        23.38        17.79        42.28 
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-A6-4105 TCGA-A6-5656 TCGA-A6-5659 
       16.04        34.65        36.53        14.53        32.91        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 
       29.16        27.09        24.13         8.38        25.08        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-3519 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       38.99         1.02         9.07        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-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 TCGA-AA-3554 
        0.99        14.01        33.99        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-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3672 TCGA-AA-3675 
       78.08         6.97        54.02        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-3837 TCGA-AA-3841 
       25.02         1.02        17.98        15.95        38.99        36.95 
TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       14.93        17.03         0.99        33.07        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3867 TCGA-AA-3870 
        0.99        31.07        53.00        17.03        24.03        29.98 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        12.99        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       24.00         2.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3979 
       16.08        50.99        13.05        34.06        25.02        24.00 
TCGA-AA-3982 TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02        19.07        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-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-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       15.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
       35.01         1.02        35.01        26.01        39.06        51.98 
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-6963 TCGA-AD-6964 TCGA-AD-A5EK TCGA-AM-5820 
        0.79         0.72         0.10         0.76         0.43         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
        0.92        14.50        27.09        16.31         0.95        15.75 
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-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-6715 TCGA-CA-6717 TCGA-CA-6718 
        3.06         2.14         3.25         0.07         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        21.01         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-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-5863 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-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
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-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.01        10.06        12.03        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-D5-6540 TCGA-D5-6541 
       15.12        17.85         4.50        17.13        16.14        15.58 
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-D5-6927 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-A1DA 
       24.43       130.65        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         5.06         2.79         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       17.29        14.76        24.13        17.95        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       13.55        19.10        12.72        37.74        10.39         8.45 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       35.01        14.01        48.03        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02        17.03         0.99        20.98         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       37.02        15.95        36.03         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       61.97        38.04         0.49         1.45         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81         6.05         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       12.99        12.00        36.00        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       10.06       126.44        41.36        57.24       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        19.96        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                        15.005                         18.050 
[1] "0.2 - 140.4 (15.0)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.5"
D66V2, continuous
D66V3, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q24.3) MUTATED    64  24
  DEL PEAK 39(17Q24.3) WILD-TYPE 365 135
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q24.3) MUTATED     64   24
  DEL PEAK 39(17Q24.3) WILD-TYPE  365  135
        clus
vv       DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  COLON                            64                            365
  RECTUM                           24                            135
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 39(17Q24.3) MUTATED        14        0        6        13         0
  DEL PEAK 39(17Q24.3) WILD-TYPE      88        1       30       152        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(17Q24.3) MUTATED           0         4          6         11
  DEL PEAK 39(17Q24.3) WILD-TYPE         3        22         16         65
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 39(17Q24.3) MUTATED           14       12         6         0
  DEL PEAK 39(17Q24.3) WILD-TYPE         38       48        19         1
D66V4, multiclass
            clus
vv           DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  STAGE I                              14                             88
  STAGE IA                              0                              1
  STAGE II                              6                             30
  STAGE IIA                            13                            152
  STAGE IIB                             0                             10
  STAGE IIC                             0                              3
  STAGE III                             4                             22
  STAGE IIIA                            6                             16
  STAGE IIIB                           11                             65
  STAGE IIIC                           14                             38
  STAGE IV                             12                             48
  STAGE IVA                             6                             19
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 39(17Q24.3) MUTATED       0  18  60  11
  DEL PEAK 39(17Q24.3) WILD-TYPE    20  87 343  51
D66V5, multiclass
       clus
vv      DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  T0+T1                            0                             20
  T2                              18                             87
  T3                              60                            343
  T4                              11                             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 39(17Q24.3) MUTATED    37  28  24
  DEL PEAK 39(17Q24.3) WILD-TYPE 298 118  84
D66V6, multiclass
    clus
vv   DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  N0                           37                            298
  N1                           28                            118
  N2                           24                             84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 39(17Q24.3) MUTATED    58  13   4   0  11
  DEL PEAK 39(17Q24.3) WILD-TYPE 385  59   5   1  47
D66V7, multiclass
     clus
vv    DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  M0                            58                            385
  M1                            13                             59
  M1A                            4                              5
  M1B                            0                              1
  MX                            11                             47
[1] 5 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q24.3) MUTATED    35  54
  DEL PEAK 39(17Q24.3) WILD-TYPE 242 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q24.3) MUTATED     35   54
  DEL PEAK 39(17Q24.3) WILD-TYPE  242  261
        clus
vv       DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  FEMALE                           35                            242
  MALE                             54                            261
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 39(17Q24.3) MUTATED                     56
  DEL PEAK 39(17Q24.3) WILD-TYPE                  317
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(17Q24.3) MUTATED                               8
  DEL PEAK 39(17Q24.3) WILD-TYPE                            47
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 39(17Q24.3) MUTATED                      21
  DEL PEAK 39(17Q24.3) WILD-TYPE                   122
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(17Q24.3) MUTATED                                2
  DEL PEAK 39(17Q24.3) WILD-TYPE                             11
D66V9, multiclass
                                clus
vv                               DEL PEAK 39(17Q24.3) MUTATED
  COLON ADENOCARCINOMA                                     56
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    21
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 39(17Q24.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      317
  COLON MUCINOUS ADENOCARCINOMA                              47
  RECTAL ADENOCARCINOMA                                     122
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D66V10, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q24.3) MUTATED     2  87
  DEL PEAK 39(17Q24.3) WILD-TYPE   7 496
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q24.3) MUTATED      2   87
  DEL PEAK 39(17Q24.3) WILD-TYPE    7  496
     clus
vv    DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  NO                             2                              7
  YES                           87                            496
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(17Q24.3) MUTATED    60   0   8   5
  DEL PEAK 39(17Q24.3) WILD-TYPE 366   5  28  22
D66V11, multiclass
    clus
vv   DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  R0                           60                            366
  R1                            0                              5
  R2                            8                             28
  RX                            5                             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"
D66V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 39(17Q24.3) MUTATED                                  1     3
  DEL PEAK 39(17Q24.3) WILD-TYPE                                0     9
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(17Q24.3) MUTATED                           5    43
  DEL PEAK 39(17Q24.3) WILD-TYPE                        39   249
D66V13, multiclass
                                  clus
vv                                 DEL PEAK 39(17Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      43
                                  clus
vv                                 DEL PEAK 39(17Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         9
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       249
[1] 4 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 40(18P11.31) MUTATION ANALYSIS
D67V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 40(18P11.31) MUTATED   278  59
  DEL PEAK 40(18P11.31) WILD-TYPE 179  47
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                            337                             226 
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                             59                              47 
$`DEL PEAK 40(18P11.31) 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-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 TCGA-A6-5656 
       37.25        34.65        36.53        14.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 
       30.44        29.19        23.61        22.09        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       27.09        24.13        25.08        25.18        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-3511 
        5.03         1.02         1.02        37.05         1.02         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3522 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 
       38.99         9.07        37.05        19.07        19.07        34.03 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3552 TCGA-AA-3553 
       29.00        26.01        14.01        33.99        13.02        24.00 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3561 TCGA-AA-3562 TCGA-AA-3660 TCGA-AA-3662 
       23.01        19.99        13.94        19.99        78.08         6.05 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 
        2.01        14.01        50.04        47.01        15.02        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       19.00        36.00        85.05        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       37.02        14.93        17.03         0.99        33.07         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-3968 TCGA-AA-3971 
       12.99        24.00        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-3989 
       50.99        13.05        34.06        26.01        24.00         7.96 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L TCGA-AA-A00O TCGA-AA-A00Q 
       13.94        19.00        34.03        17.03        27.02        42.02 
TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
       14.99        21.99        15.02        15.02        32.02        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
        1.02        33.04        26.01         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 
        5.03        41.00        40.96         4.21         0.79         1.58 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 
        1.02         0.10         0.20         0.43        14.50         0.95 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 
       15.75         5.19         5.52        75.25         5.65         5.13 
TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 
       83.80        22.36        65.00        62.79        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        5.23         1.94         2.24         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 
        0.26         1.35        48.20        21.99         2.01         8.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
        8.02        13.02        29.06        22.03        30.08         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        14.04        29.03        16.04        21.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       13.02        15.02        11.01        11.08        11.01        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-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       18.25         1.32        17.85        17.13        12.49         7.53 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD 
       12.43        14.30         9.04        13.41        11.38        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB 
       38.20       130.65        13.32        12.59       140.38        44.32 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
      139.17        26.47       119.93        35.97       117.07        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        11.11        13.45         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 
       16.24        33.67         1.28         0.53        35.41        28.21 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6310 
        8.35        82.39        23.51        61.87        55.04        45.11 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       36.72        36.00        91.79        46.75        47.15         4.11 
TCGA-NH-A50V TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        5.06        26.99        17.29        24.13        17.95        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       43.04        13.55        12.72        37.74        10.39        14.50 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       20.02        36.03         7.07         1.02         2.01        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
       46.03        34.03        50.04         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 
        7.99        29.98         1.02        32.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        1.02        36.95        17.03        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        36.03         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 
        0.99        13.94         6.02        25.97        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 
        9.07         1.02        12.00        31.00        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       51.98         1.94        41.00        38.04         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        0.49         2.40        20.55        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31        16.41        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       13.64        11.97        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        1.02         0.66         0.69         0.76         0.46        18.28 
TCGA-G5-6235 
       55.76 

$`DEL PEAK 40(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        21.01         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-AF-2693 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
        5.59        14.76        19.10         8.45        15.39        10.39 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3599 
       12.00        32.02         8.02         1.02         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 
        6.05        19.99         0.99         0.99        13.02        14.01 
TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A01Y TCGA-AG-A025 
       14.04        20.98        23.01        36.03        64.01        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 
       38.96        61.97         1.45         1.81         5.29        32.61 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       19.96        20.91         8.61        17.46         8.45         9.96 
TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6572 TCGA-G5-6641 
        0.53         1.12        47.08        26.43 

  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                         140.38                          135.65 
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                         17.230                          18.545 
[1] "0.1 - 140.4 (17.2)" "0.1 - 135.7 (18.5)"
[1] "hr=" "1.1"
D67V2, continuous
D67V3, binary
                                 cls
clus                                0   1
  DEL PEAK 40(18P11.31) MUTATED   230 119
  DEL PEAK 40(18P11.31) WILD-TYPE 199  40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.31) MUTATED    230  119
  DEL PEAK 40(18P11.31) WILD-TYPE  199   40
        clus
vv       DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  COLON                            230                             199
  RECTUM                           119                              40
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 40(18P11.31) MUTATED        56        0       14        91         4
  DEL PEAK 40(18P11.31) WILD-TYPE      46        1       22        74         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18P11.31) MUTATED           3        12         14         49
  DEL PEAK 40(18P11.31) WILD-TYPE         0        14          8         27
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 40(18P11.31) MUTATED           33       46        22         0
  DEL PEAK 40(18P11.31) WILD-TYPE         19       14         3         1
D67V4, multiclass
            clus
vv           DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  STAGE I                               56                              46
  STAGE IA                               0                               1
  STAGE II                              14                              22
  STAGE IIA                             91                              74
  STAGE IIB                              4                               6
  STAGE IIC                              3                               0
  STAGE III                             12                              14
  STAGE IIIA                            14                               8
  STAGE IIIB                            49                              27
  STAGE IIIC                            33                              19
  STAGE IV                              46                              14
  STAGE IVA                             22                               3
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  DEL PEAK 40(18P11.31) MUTATED      11  61 243  37
  DEL PEAK 40(18P11.31) WILD-TYPE     9  44 160  25
D67V5, multiclass
       clus
vv      DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  T0+T1                            11                               9
  T2                               61                              44
  T3                              243                             160
  T4                               37                              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
  DEL PEAK 40(18P11.31) MUTATED   182 100  68
  DEL PEAK 40(18P11.31) WILD-TYPE 153  46  40
D67V6, multiclass
    clus
vv   DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  N0                           182                             153
  N1                           100                              46
  N2                            68                              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 40(18P11.31) MUTATED   250  58   9   0  31
  DEL PEAK 40(18P11.31) WILD-TYPE 193  14   0   1  27
D67V7, multiclass
     clus
vv    DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  M0                            250                             193
  M1                             58                              14
  M1A                             9                               0
  M1B                             0                               1
  MX                             31                              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"
D67V8, binary
                                 cls
clus                                0   1
  DEL PEAK 40(18P11.31) MUTATED   163 189
  DEL PEAK 40(18P11.31) WILD-TYPE 114 126
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.31) MUTATED    163  189
  DEL PEAK 40(18P11.31) WILD-TYPE  114  126
        clus
vv       DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  FEMALE                           163                             114
  MALE                             189                             126
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 40(18P11.31) MUTATED                    222
  DEL PEAK 40(18P11.31) WILD-TYPE                  151
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 40(18P11.31) MUTATED                               7
  DEL PEAK 40(18P11.31) WILD-TYPE                            48
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 40(18P11.31) MUTATED                     113
  DEL PEAK 40(18P11.31) WILD-TYPE                    30
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 40(18P11.31) MUTATED                                6
  DEL PEAK 40(18P11.31) WILD-TYPE                              7
D67V9, multiclass
                                clus
vv                               DEL PEAK 40(18P11.31) MUTATED
  COLON ADENOCARCINOMA                                     222
  COLON MUCINOUS ADENOCARCINOMA                              7
  RECTAL ADENOCARCINOMA                                    113
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 40(18P11.31) WILD-TYPE
  COLON ADENOCARCINOMA                                       151
  COLON MUCINOUS ADENOCARCINOMA                               48
  RECTAL ADENOCARCINOMA                                       30
  RECTAL MUCINOUS ADENOCARCINOMA                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, binary
                                 cls
clus                                0   1
  DEL PEAK 40(18P11.31) MUTATED     7 345
  DEL PEAK 40(18P11.31) WILD-TYPE   2 238
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.31) MUTATED      7  345
  DEL PEAK 40(18P11.31) WILD-TYPE    2  238
     clus
vv    DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  NO                              7                               2
  YES                           345                             238
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 40(18P11.31) MUTATED   249   2  29  13
  DEL PEAK 40(18P11.31) WILD-TYPE 177   3   7  14
D67V11, multiclass
    clus
vv   DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  R0                           249                             177
  R1                             2                               3
  R2                            29                               7
  RX                            13                              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"
D67V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 40(18P11.31) MUTATED                                  1     6
  DEL PEAK 40(18P11.31) WILD-TYPE                                0     6
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(18P11.31) MUTATED                          25   180
  DEL PEAK 40(18P11.31) WILD-TYPE                        19   112
D67V13, multiclass
                                  clus
vv                                 DEL PEAK 40(18P11.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        6
  BLACK OR AFRICAN AMERICAN                                   25
  WHITE                                                      180
                                  clus
vv                                 DEL PEAK 40(18P11.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          6
  BLACK OR AFRICAN AMERICAN                                     19
  WHITE                                                        112
[1] 4 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 41(18Q12.2) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(18Q12.2) MUTATED   309  69
  DEL PEAK 41(18Q12.2) WILD-TYPE 148  37
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           378                            185 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                            69                             37 
$`DEL PEAK 41(18Q12.2) 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-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 
       32.91        31.63        30.44        29.19        23.61        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 
       29.16        27.09        22.52        24.13        25.18        20.61 
TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       21.76        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-3511 
        5.03         1.02         1.02        37.05         1.02         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3526 
       38.99         9.07        24.03        37.05        36.03        19.07 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       19.07        34.03        29.00        26.01        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-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3662 TCGA-AA-3666 
       13.94        19.99        61.02        78.08         6.05         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 
       14.01        50.04        47.01        15.02         5.98        37.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       19.00        36.00        85.05        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 
       37.02        14.93        17.03         0.99        33.07         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-3875 TCGA-AA-3939 TCGA-AA-3941 TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 
       18.05        12.99        24.00         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-3979 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       24.00        27.02         7.96        19.00        34.03        18.05 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C 
       42.02        17.03        14.99        21.99        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X 
        0.99        32.02        31.00         1.02        33.04        26.01 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02         2.96        39.98         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       41.00        40.96         4.21         0.79         1.58         1.02 
TCGA-AD-6963 TCGA-AD-6964 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
        0.10         0.76         0.20         0.43         0.46        14.50 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4616 
       16.31        15.75         5.19         5.52        75.25         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-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 
       29.56         5.23         1.94         2.24         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 
        0.07         0.26         1.35       102.44        48.20        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        2.01         8.02         8.02        27.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       22.03        30.08         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       29.03        16.04        21.99        13.02        15.02        11.01 
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-D5-6532 
       12.26        19.59        13.51        11.51        20.19        18.25 
TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
        1.32        17.85        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-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-A282 
       12.59       140.38         7.50        44.32       131.51       139.17 
TCGA-DM-A285 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
        6.12        26.47       119.93       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       13.38        11.11        13.45         1.55        16.31        29.59 
TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 
       16.24         1.28         0.53        35.41        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-G4-6625 TCGA-G4-6626 
       39.42        35.93        36.72        36.00        91.79        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-QG-A5YV TCGA-QG-A5YX TCGA-AF-2687 
       47.15         4.11         5.06        26.99        17.29        24.13 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
       24.00        46.03        34.03         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98         1.94        38.96        41.00        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         4.60        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         7.10        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       11.51        10.78        13.64        11.97         8.45        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

$`DEL PEAK 41(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        21.01         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-A288 TCGA-DM-A28C 
       10.26       119.70       135.65         7.76        14.04        81.37 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       35.97        60.79        98.24        13.64         6.18        35.87 
TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       33.67        19.43       107.67        74.56        43.07        53.62 
TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       51.75        26.43        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5Z2 
       26.17        52.80         2.79         5.98         5.59        14.76 
TCGA-AF-5654 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 
        8.45         8.02         1.02        12.03        19.99         0.99 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A025 
       13.02        14.01        20.98        36.03         9.07        49.97 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 
       61.97         1.45         1.81         5.29        32.61        19.96 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46         9.96         0.53         1.12 

  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                         17.49                          18.05 
[1] "0.1 - 140.4 (17.5)" "0.1 - 135.7 (18.1)"
[1] "hr=" "1.1"
D68V2, continuous
D68V3, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q12.2) MUTATED   257 136
  DEL PEAK 41(18Q12.2) WILD-TYPE 172  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED    257  136
  DEL PEAK 41(18Q12.2) WILD-TYPE  172   23
        clus
vv       DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  COLON                           257                            172
  RECTUM                          136                             23
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 41(18Q12.2) MUTATED        59        0       21       100         4
  DEL PEAK 41(18Q12.2) WILD-TYPE      43        1       15        65         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(18Q12.2) MUTATED           3        15         18         56
  DEL PEAK 41(18Q12.2) WILD-TYPE         0        11          4         20
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 41(18Q12.2) MUTATED           38       51        21         0
  DEL PEAK 41(18Q12.2) WILD-TYPE         14        9         4         1
D68V4, multiclass
            clus
vv           DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  STAGE I                              59                             43
  STAGE IA                              0                              1
  STAGE II                             21                             15
  STAGE IIA                           100                             65
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            15                             11
  STAGE IIIA                           18                              4
  STAGE IIIB                           56                             20
  STAGE IIIC                           38                             14
  STAGE IV                             51                              9
  STAGE IVA                            21                              4
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 41(18Q12.2) MUTATED      11  67 278  39
  DEL PEAK 41(18Q12.2) WILD-TYPE     9  38 125  23
D68V5, multiclass
       clus
vv      DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  T0+T1                           11                              9
  T2                              67                             38
  T3                             278                            125
  T4                              39                             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
  DEL PEAK 41(18Q12.2) MUTATED   200 112  81
  DEL PEAK 41(18Q12.2) WILD-TYPE 135  34  27
D68V6, multiclass
    clus
vv   DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  N0                          200                            135
  N1                          112                             34
  N2                           81                             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
  DEL PEAK 41(18Q12.2) MUTATED   287  61   8   0  35
  DEL PEAK 41(18Q12.2) WILD-TYPE 156  11   1   1  23
D68V7, multiclass
     clus
vv    DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  M0                           287                            156
  M1                            61                             11
  M1A                            8                              1
  M1B                            0                              1
  MX                            35                             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"
D68V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q12.2) MUTATED   180 216
  DEL PEAK 41(18Q12.2) WILD-TYPE  97  99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED    180  216
  DEL PEAK 41(18Q12.2) WILD-TYPE   97   99
        clus
vv       DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  FEMALE                          180                             97
  MALE                            216                             99
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 41(18Q12.2) MUTATED                    245
  DEL PEAK 41(18Q12.2) WILD-TYPE                  128
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(18Q12.2) MUTATED                              11
  DEL PEAK 41(18Q12.2) WILD-TYPE                            44
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 41(18Q12.2) MUTATED                     125
  DEL PEAK 41(18Q12.2) WILD-TYPE                    18
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(18Q12.2) MUTATED                               10
  DEL PEAK 41(18Q12.2) WILD-TYPE                              3
D68V9, multiclass
                                clus
vv                               DEL PEAK 41(18Q12.2) MUTATED
  COLON ADENOCARCINOMA                                    245
  COLON MUCINOUS ADENOCARCINOMA                            11
  RECTAL ADENOCARCINOMA                                   125
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 41(18Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      128
  COLON MUCINOUS ADENOCARCINOMA                              44
  RECTAL ADENOCARCINOMA                                      18
  RECTAL MUCINOUS ADENOCARCINOMA                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q12.2) MUTATED     9 387
  DEL PEAK 41(18Q12.2) WILD-TYPE   0 196
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED      9  387
  DEL PEAK 41(18Q12.2) WILD-TYPE    0  196
     clus
vv    DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  NO                             9                              0
  YES                          387                            196
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(18Q12.2) MUTATED   282   3  29  13
  DEL PEAK 41(18Q12.2) WILD-TYPE 144   2   7  14
D68V11, multiclass
    clus
vv   DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  R0                          282                            144
  R1                            3                              2
  R2                           29                              7
  RX                           13                             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"
D68V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 41(18Q12.2) MUTATED                                  1     6
  DEL PEAK 41(18Q12.2) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(18Q12.2) MUTATED                          25   202
  DEL PEAK 41(18Q12.2) WILD-TYPE                        19    90
D68V13, multiclass
                                  clus
vv                                 DEL PEAK 41(18Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  25
  WHITE                                                     202
                                  clus
vv                                 DEL PEAK 41(18Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    19
  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(69) Variable = DEL PEAK 42(18Q21.2) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(18Q21.2) MUTATED   323  73
  DEL PEAK 42(18Q21.2) WILD-TYPE 134  33
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           396                            167 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            73                             33 
$`DEL PEAK 42(18Q21.2) 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-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
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-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       20.61        21.76        24.39        23.87        20.28        61.84 
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-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02         6.97        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       36.03        19.07        19.07        34.03        29.00        26.01 
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-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       15.02         5.98        37.05        19.00        36.00        85.05 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       25.02        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3866 
        0.99        33.07         0.99        31.07        31.07        17.03 
TCGA-AA-3867 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 TCGA-AA-3939 TCGA-AA-3941 
       24.03        27.02        29.98        18.05        12.99        24.00 
TCGA-AA-3952 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3972 
        2.01        20.98        34.03        21.99        16.08        50.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3982 TCGA-AA-3989 
       13.05        34.06        26.01        24.00        27.02         7.96 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       19.00        34.03        18.05        42.02        17.03        14.99 
TCGA-AA-A00Z TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K 
       21.99        15.02        15.02         0.99        32.02        31.00 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F 
        1.02        33.04        26.01        37.02         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6888 
        2.01         5.03         0.92        41.00        40.96         4.21 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
        0.79         1.58         1.02         0.10         0.20         0.43 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D 
        0.46        14.50        16.31        15.75         5.19         5.52 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 TCGA-AZ-4684 
       75.25         5.65         5.13        83.80        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        61.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        3.19         1.94         2.24         2.14         3.29         0.07 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        0.26         1.35       102.44        48.20        21.99         2.01 
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-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-6675 
       16.04        21.99        13.02        15.02        11.01        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-D5-6531 
       12.26        19.59        13.51        11.51        20.19        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       18.25         1.32        17.85        17.13        12.49        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-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       11.38        24.43        38.20       130.65        92.75        49.91 
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-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-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-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       13.45         1.55        16.31        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6297 
        1.28         0.53        35.41        28.21         8.35        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-G4-6322 TCGA-G4-6625 
       39.42        35.93        36.72        36.00        26.04        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV 
       46.75        47.15         4.11         5.06         5.98        26.99 
TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       17.29        24.13        17.95        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       19.10        12.72        37.74        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       20.02        10.39        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
        2.01        50.04         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
       19.99         1.02        36.95        17.03        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03         0.99        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        15.95         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 
       31.00        70.03        64.01        10.98        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       38.96        41.00        38.04         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       11.51        10.78        13.64        11.97         8.45        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

$`DEL PEAK 42(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-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 
        0.95         0.20        21.44        17.82        50.37        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6601 TCGA-CA-5255 
        1.41        32.94        49.41         6.77       100.01         3.06 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        3.25         0.33         0.10        17.56        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        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       20.02        37.02        26.04        22.98        16.01        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       15.02        15.02        12.00        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 
       12.95        20.42         7.92        15.12         4.50        16.14 
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-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-F4-6463 
      119.70       135.65         7.76        81.37        60.79        13.64 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 
        6.18        35.87        19.43       107.67        43.07        53.62 
TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6321 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 
       51.75        26.43        22.09        13.78        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5Z2 TCGA-AF-5654 TCGA-AG-3580 
       52.80         2.79         5.59        14.76         8.45         8.02 
TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 
       12.03        19.99         0.99        13.02        14.01        20.98 
TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-DY-A1H8 TCGA-EI-6507 
       36.03        49.97        61.97         1.45        32.61        19.96 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46         9.96         0.53         1.12 

  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                         17.49                          19.04 
[1] "0.1 - 140.4 (17.5)" "0.1 - 135.7 (19.0)"
[1] "hr=" "1.1"
D69V2, continuous
D69V3, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED   271 140
  DEL PEAK 42(18Q21.2) WILD-TYPE 158  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED    271  140
  DEL PEAK 42(18Q21.2) WILD-TYPE  158   19
        clus
vv       DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  COLON                           271                            158
  RECTUM                          140                             19
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 42(18Q21.2) MUTATED        61        0       23       102         4
  DEL PEAK 42(18Q21.2) WILD-TYPE      41        1       13        63         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(18Q21.2) MUTATED           3        16         18         59
  DEL PEAK 42(18Q21.2) WILD-TYPE         0        10          4         17
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 42(18Q21.2) MUTATED           42       54        22         1
  DEL PEAK 42(18Q21.2) WILD-TYPE         10        6         3         0
D69V4, multiclass
            clus
vv           DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  STAGE I                              61                             41
  STAGE IA                              0                              1
  STAGE II                             23                             13
  STAGE IIA                           102                             63
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            16                             10
  STAGE IIIA                           18                              4
  STAGE IIIB                           59                             17
  STAGE IIIC                           42                             10
  STAGE IV                             54                              6
  STAGE IVA                            22                              3
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 42(18Q21.2) MUTATED      12  68 290  43
  DEL PEAK 42(18Q21.2) WILD-TYPE     8  37 113  19
D69V5, multiclass
       clus
vv      DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  T0+T1                           12                              8
  T2                              68                             37
  T3                             290                            113
  T4                              43                             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
  DEL PEAK 42(18Q21.2) MUTATED   206 116  89
  DEL PEAK 42(18Q21.2) WILD-TYPE 129  30  19
D69V6, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  N0                          206                            129
  N1                          116                             30
  N2                           89                             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 42(18Q21.2) MUTATED   298  65   8   1  38
  DEL PEAK 42(18Q21.2) WILD-TYPE 145   7   1   0  20
D69V7, multiclass
     clus
vv    DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  M0                           298                            145
  M1                            65                              7
  M1A                            8                              1
  M1B                            1                              0
  MX                            38                             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"
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED   184 230
  DEL PEAK 42(18Q21.2) WILD-TYPE  93  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED    184  230
  DEL PEAK 42(18Q21.2) WILD-TYPE   93   85
        clus
vv       DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  FEMALE                          184                             93
  MALE                            230                             85
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                    256
  DEL PEAK 42(18Q21.2) WILD-TYPE                  117
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                              14
  DEL PEAK 42(18Q21.2) WILD-TYPE                            41
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                     126
  DEL PEAK 42(18Q21.2) WILD-TYPE                    17
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                               12
  DEL PEAK 42(18Q21.2) WILD-TYPE                              1
D69V9, multiclass
                                clus
vv                               DEL PEAK 42(18Q21.2) MUTATED
  COLON ADENOCARCINOMA                                    256
  COLON MUCINOUS ADENOCARCINOMA                            14
  RECTAL ADENOCARCINOMA                                   126
  RECTAL MUCINOUS ADENOCARCINOMA                           12
                                clus
vv                               DEL PEAK 42(18Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      117
  COLON MUCINOUS ADENOCARCINOMA                              41
  RECTAL ADENOCARCINOMA                                      17
  RECTAL MUCINOUS ADENOCARCINOMA                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED     9 405
  DEL PEAK 42(18Q21.2) WILD-TYPE   0 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED      9  405
  DEL PEAK 42(18Q21.2) WILD-TYPE    0  178
     clus
vv    DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  NO                             9                              0
  YES                          405                            178
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(18Q21.2) MUTATED   292   3  30  14
  DEL PEAK 42(18Q21.2) WILD-TYPE 134   2   6  13
D69V11, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  R0                          292                            134
  R1                            3                              2
  R2                           30                              6
  RX                           14                             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"
D69V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 42(18Q21.2) MUTATED                                  1     7
  DEL PEAK 42(18Q21.2) WILD-TYPE                                0     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 42(18Q21.2) MUTATED                          28   213
  DEL PEAK 42(18Q21.2) WILD-TYPE                        16    79
D69V13, multiclass
                                  clus
vv                                 DEL PEAK 42(18Q21.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       7
  BLACK OR AFRICAN AMERICAN                                  28
  WHITE                                                     213
                                  clus
vv                                 DEL PEAK 42(18Q21.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    16
  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(70) Variable = DEL PEAK 43(18Q22.1) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(18Q22.1) MUTATED   319  73
  DEL PEAK 43(18Q22.1) WILD-TYPE 138  33
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                           392                            171 
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                            73                             33 
$`DEL PEAK 43(18Q22.1) 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-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2683 TCGA-A6-2684 
       44.91        35.11        45.60        13.94        15.52        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4105 TCGA-A6-4107 
       37.25        16.04        34.65        36.53        14.53        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        30.44        29.19        23.61        22.09 
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-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       20.61        21.76        24.39        23.87        20.28        61.84 
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-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3520 TCGA-AA-3522 
        1.02         6.97        38.99         9.07        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3526 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3532 TCGA-AA-3538 
       36.03        19.07        19.07        34.03        29.00        26.01 
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-3561 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 
       23.01        19.99        13.94        19.99        61.02        78.08 
TCGA-AA-3662 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
        6.05        54.02         2.01        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       15.02         5.98        37.05        19.00        36.00        85.05 
TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 
       25.02        38.99        36.95        37.02        14.93        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3860 TCGA-AA-3864 
        0.99        33.07         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-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-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U 
        7.96        13.94        19.00        34.03        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-A54L 
        0.43         0.46        14.50        16.31        15.75         5.19 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4681 TCGA-AZ-4682 
        5.52        75.25         5.65         5.13        83.80        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        61.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-AZ-6608 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 
       11.74         3.19         1.94         2.24         2.14         3.29 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5912 TCGA-CK-5914 TCGA-CK-6748 
        0.07         0.26         1.35        48.20        21.99         2.01 
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-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-6675 
       16.04        21.99        13.02        15.02        11.01        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-D5-6531 
       12.26        19.59        13.51        11.51        20.19        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 
       18.25         1.32        15.12        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-A28F TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       35.97       117.07        98.24        95.18         8.61        13.38 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       11.11        13.45         1.55        16.31        29.59        16.24 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6294 TCGA-G4-6295 
       33.67         1.28         0.53        35.41        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-G4-6625 
       45.11        39.42        35.93        36.72        36.00        91.79 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV 
       46.75        47.15         4.11         5.06         5.98        26.99 
TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       17.29        24.13        17.95        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       19.10        12.72        37.74        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       20.02        10.39        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        1.02         2.01        24.00        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       50.04         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
        0.99        29.98        32.98         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       36.95        17.03        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       15.95         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       64.01        10.98        51.98         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 
       38.04         0.49         0.69         0.72         4.60        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         0.49         2.40        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.31        16.41        11.51        10.78        13.64        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.69         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`DEL PEAK 43(18Q22.1) 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-3877 
        1.02        17.98        15.95        36.03        32.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3966 TCGA-AA-3977 
        2.01        33.01        26.01        24.00         2.01        25.02 
TCGA-AA-3986 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       19.07        27.02        38.04        30.02        18.05        18.05 
TCGA-AA-A00L TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G 
       17.03         4.01        27.02         0.99        34.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A024 
       31.00        38.07         1.02        35.01        35.01        39.06 
TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 
       51.98        22.03        39.98        18.05         0.07        21.37 
TCGA-AD-6889 TCGA-AD-6895 TCGA-AD-6964 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       56.55         0.72         0.76         0.92        27.09         0.95 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 
        0.20        21.44        17.82        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-4948 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10        17.56       102.44        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        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       20.02        37.02        26.04        22.98        16.01        15.02 
TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 
       15.02        15.02        12.00        14.99        12.99        14.04 
TCGA-CM-6674 TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 
       12.95        20.42         7.92         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-G4-6322 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-A6GB TCGA-QG-A5Z2 TCGA-AF-5654 TCGA-AG-3580 
       52.80         2.79         5.59        14.76         8.45         8.02 
TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3892 
        1.02        12.03        19.99         1.02         0.99        13.02 
TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 
       14.01        20.98        36.03        49.97        61.97         1.45 
TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 
        1.81         5.29        32.61        19.96         8.61        17.46 
TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
        9.96         0.53         1.12 

  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                        140.38                         135.65 
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                         17.49                          18.05 
[1] "0.1 - 140.4 (17.5)" "0.1 - 135.7 (18.1)"
[1] "hr=" "1"  
D70V2, continuous
D70V3, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q22.1) MUTATED   271 135
  DEL PEAK 43(18Q22.1) WILD-TYPE 158  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.1) MUTATED    271  135
  DEL PEAK 43(18Q22.1) WILD-TYPE  158   24
        clus
vv       DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  COLON                           271                            158
  RECTUM                          135                             24
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 43(18Q22.1) MUTATED        61        0       23       102         4
  DEL PEAK 43(18Q22.1) WILD-TYPE      41        1       13        63         6
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(18Q22.1) MUTATED           3        14         17         58
  DEL PEAK 43(18Q22.1) WILD-TYPE         0        12          5         18
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 43(18Q22.1) MUTATED           42       53        22         1
  DEL PEAK 43(18Q22.1) WILD-TYPE         10        7         3         0
D70V4, multiclass
            clus
vv           DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  STAGE I                              61                             41
  STAGE IA                              0                              1
  STAGE II                             23                             13
  STAGE IIA                           102                             63
  STAGE IIB                             4                              6
  STAGE IIC                             3                              0
  STAGE III                            14                             12
  STAGE IIIA                           17                              5
  STAGE IIIB                           58                             18
  STAGE IIIC                           42                             10
  STAGE IV                             53                              7
  STAGE IVA                            22                              3
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 43(18Q22.1) MUTATED      12  68 285  43
  DEL PEAK 43(18Q22.1) WILD-TYPE     8  37 118  19
D70V5, multiclass
       clus
vv      DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  T0+T1                           12                              8
  T2                              68                             37
  T3                             285                            118
  T4                              43                             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
  DEL PEAK 43(18Q22.1) MUTATED   206 112  88
  DEL PEAK 43(18Q22.1) WILD-TYPE 129  34  20
D70V6, multiclass
    clus
vv   DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  N0                          206                            129
  N1                          112                             34
  N2                           88                             20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 43(18Q22.1) MUTATED   295  64   8   1  37
  DEL PEAK 43(18Q22.1) WILD-TYPE 148   8   1   0  21
D70V7, multiclass
     clus
vv    DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  M0                           295                            148
  M1                            64                              8
  M1A                            8                              1
  M1B                            1                              0
  MX                            37                             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"
D70V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q22.1) MUTATED   183 226
  DEL PEAK 43(18Q22.1) WILD-TYPE  94  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.1) MUTATED    183  226
  DEL PEAK 43(18Q22.1) WILD-TYPE   94   89
        clus
vv       DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  FEMALE                          183                             94
  MALE                            226                             89
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 43(18Q22.1) MUTATED                    257
  DEL PEAK 43(18Q22.1) WILD-TYPE                  116
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(18Q22.1) MUTATED                              13
  DEL PEAK 43(18Q22.1) WILD-TYPE                            42
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 43(18Q22.1) MUTATED                     124
  DEL PEAK 43(18Q22.1) WILD-TYPE                    19
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(18Q22.1) MUTATED                               10
  DEL PEAK 43(18Q22.1) WILD-TYPE                              3
D70V9, multiclass
                                clus
vv                               DEL PEAK 43(18Q22.1) MUTATED
  COLON ADENOCARCINOMA                                    257
  COLON MUCINOUS ADENOCARCINOMA                            13
  RECTAL ADENOCARCINOMA                                   124
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 43(18Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      116
  COLON MUCINOUS ADENOCARCINOMA                              42
  RECTAL ADENOCARCINOMA                                      19
  RECTAL MUCINOUS ADENOCARCINOMA                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q22.1) MUTATED     9 400
  DEL PEAK 43(18Q22.1) WILD-TYPE   0 183
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.1) MUTATED      9  400
  DEL PEAK 43(18Q22.1) WILD-TYPE    0  183
     clus
vv    DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  NO                             9                              0
  YES                          400                            183
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(18Q22.1) MUTATED   289   3  29  14
  DEL PEAK 43(18Q22.1) WILD-TYPE 137   2   7  13
D70V11, multiclass
    clus
vv   DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  R0                          289                            137
  R1                            3                              2
  R2                           29                              7
  RX                           14                             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"
D70V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 43(18Q22.1) MUTATED                                  1     6
  DEL PEAK 43(18Q22.1) WILD-TYPE                                0     6
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 43(18Q22.1) MUTATED                          28   210
  DEL PEAK 43(18Q22.1) WILD-TYPE                        16    82
D70V13, multiclass
                                  clus
vv                                 DEL PEAK 43(18Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       6
  BLACK OR AFRICAN AMERICAN                                  28
  WHITE                                                     210
                                  clus
vv                                 DEL PEAK 43(18Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         6
  BLACK OR AFRICAN AMERICAN                                    16
  WHITE                                                        82
[1] 4 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(71) Variable = DEL PEAK 44(19P13.3) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(19P13.3) MUTATED    66  20
  DEL PEAK 44(19P13.3) WILD-TYPE 391  86
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            86                            477 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            20                             86 
$`DEL PEAK 44(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-AF-2687 TCGA-AF-2689 TCGA-AF-4110 
        8.35        82.39        36.00        24.13        17.95        14.50 
TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3608 TCGA-AG-3732 TCGA-AG-3893 TCGA-AG-4008 
       12.00         1.02        15.95        32.98        35.01        17.03 
TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01Y TCGA-CI-6619 TCGA-CI-6620 TCGA-CL-4957 
       15.95         9.07        64.01         6.05         6.05        13.97 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF 
       12.99        13.97         7.10         5.29       129.27        24.13 
TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6885 TCGA-F5-6571 TCGA-F5-6702 
       51.48        17.00        16.34        13.64        31.30        14.86 
TCGA-F5-6810 TCGA-G5-6233 
        0.39        18.28 

$`DEL PEAK 44(19P13.3) 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-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4105 
       15.52        37.05        37.25        16.04        36.53        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-A6-6648 TCGA-A6-6649 TCGA-A6-6650 
       22.52        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-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        52.44         9.63         5.03         1.02 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3496 TCGA-AA-3502 TCGA-AA-3510 
        3.02         1.02        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-3520 
        6.97         1.02        13.02        38.99         1.02        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-3543 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00         0.99        14.01        33.99        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-3664 TCGA-AA-3667 TCGA-AA-3672 
       61.02        78.08         6.97        54.02        14.01         0.92 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       50.04        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3688 TCGA-AA-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       37.05        19.00         5.03        85.05        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-3844 TCGA-AA-3846 TCGA-AA-3848 
       17.98        15.95        38.99        14.93        17.03         0.99 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07        36.03        32.05         0.99        31.07        53.00 
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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       26.01        24.00        20.98        34.03         2.01        21.99 
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-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-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-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        15.02        32.02        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-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98         2.96         2.01         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-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-3779 TCGA-AU-6004 TCGA-AY-4071 
        0.43         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-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        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-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 
        2.24         3.06         2.14         3.25         0.07         0.26 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
        0.33         0.10         1.35        17.56        40.34        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        21.01         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-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 
        8.02        27.02        13.02        29.06        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-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-6680 TCGA-D5-5538 
       12.95        11.08        11.08        11.01        12.03        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-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
        7.92        15.12        17.85        17.13        12.49        16.14 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
        7.53        12.39        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-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-A1HB TCGA-DM-A280 TCGA-DM-A282 
       12.59       140.38         7.50       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-F4-6460 
       60.79       117.07        98.24        95.18         8.61        13.38 
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-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       29.59        16.24         1.28         0.53        35.41        19.43 
TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      107.67        28.21        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-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV 
        4.11         5.06         2.79         5.98         5.59        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       17.29        14.76        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       12.72        37.74        10.39         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       10.39        36.03        32.02         8.02         7.07         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         6.05         0.99        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98         1.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        17.03        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       23.01        37.02        36.03         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 
        0.72         4.60         1.81        10.19         6.97         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       12.00        15.02        36.00        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 
       10.06       126.44        41.36        57.24        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 
       17.46        11.97         8.45         9.96        37.51         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                         17.03                          17.98 
[1] "0.2 - 131.5 (17.0)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.2"
D71V2, continuous
D71V3, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    59  33
  DEL PEAK 44(19P13.3) WILD-TYPE 370 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     59   33
  DEL PEAK 44(19P13.3) WILD-TYPE  370  126
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  COLON                            59                            370
  RECTUM                           33                            126
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 44(19P13.3) MUTATED        11        0        4        18         0
  DEL PEAK 44(19P13.3) WILD-TYPE      91        1       32       147        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(19P13.3) MUTATED           1         5          6          8
  DEL PEAK 44(19P13.3) WILD-TYPE         2        21         16         68
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 44(19P13.3) MUTATED           15       15         7         1
  DEL PEAK 44(19P13.3) WILD-TYPE         37       45        18         0
D71V4, multiclass
            clus
vv           DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  STAGE I                              11                             91
  STAGE IA                              0                              1
  STAGE II                              4                             32
  STAGE IIA                            18                            147
  STAGE IIB                             0                             10
  STAGE IIC                             1                              2
  STAGE III                             5                             21
  STAGE IIIA                            6                             16
  STAGE IIIB                            8                             68
  STAGE IIIC                           15                             37
  STAGE IV                             15                             45
  STAGE IVA                             7                             18
  STAGE IVB                             1                              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                             T0+T1  T2  T3  T4
  DEL PEAK 44(19P13.3) MUTATED       1  13  70   9
  DEL PEAK 44(19P13.3) WILD-TYPE    19  92 333  53
D71V5, multiclass
       clus
vv      DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  T0+T1                            1                             19
  T2                              13                             92
  T3                              70                            333
  T4                               9                             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"
                                vv
clus                              N0  N1  N2
  DEL PEAK 44(19P13.3) MUTATED    36  27  30
  DEL PEAK 44(19P13.3) WILD-TYPE 299 119  78
D71V6, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  N0                           36                            299
  N1                           27                            119
  N2                           30                             78
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 44(19P13.3) MUTATED    62  19   2   1   8
  DEL PEAK 44(19P13.3) WILD-TYPE 381  53   7   0  50
D71V7, multiclass
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  M0                            62                            381
  M1                            19                             53
  M1A                            2                              7
  M1B                            1                              0
  MX                             8                             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"
D71V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    40  53
  DEL PEAK 44(19P13.3) WILD-TYPE 237 262
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     40   53
  DEL PEAK 44(19P13.3) WILD-TYPE  237  262
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  FEMALE                           40                            237
  MALE                             53                            262
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                     54
  DEL PEAK 44(19P13.3) WILD-TYPE                  319
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                               4
  DEL PEAK 44(19P13.3) WILD-TYPE                            51
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                      31
  DEL PEAK 44(19P13.3) WILD-TYPE                   112
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                                1
  DEL PEAK 44(19P13.3) WILD-TYPE                             12
D71V9, multiclass
                                clus
vv                               DEL PEAK 44(19P13.3) MUTATED
  COLON ADENOCARCINOMA                                     54
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    31
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 44(19P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      319
  COLON MUCINOUS ADENOCARCINOMA                              51
  RECTAL ADENOCARCINOMA                                     112
  RECTAL MUCINOUS ADENOCARCINOMA                             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"
D71V10, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED     2  91
  DEL PEAK 44(19P13.3) WILD-TYPE   7 492
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      2   91
  DEL PEAK 44(19P13.3) WILD-TYPE    7  492
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  NO                             2                              7
  YES                           91                            492
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(19P13.3) MUTATED    60   1  10   4
  DEL PEAK 44(19P13.3) WILD-TYPE 366   4  26  23
D71V11, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  R0                           60                            366
  R1                            1                              4
  R2                           10                             26
  RX                            4                             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"
D71V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 44(19P13.3) MUTATED                                  0     2
  DEL PEAK 44(19P13.3) WILD-TYPE                                1    10
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 44(19P13.3) MUTATED                           5    42
  DEL PEAK 44(19P13.3) WILD-TYPE                        39   250
D71V13, multiclass
                                  clus
vv                                 DEL PEAK 44(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   5
  WHITE                                                      42
                                  clus
vv                                 DEL PEAK 44(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        10
  BLACK OR AFRICAN AMERICAN                                    39
  WHITE                                                       250
[1] 4 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(72) Variable = DEL PEAK 45(20P12.1) MUTATION ANALYSIS
D72V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(20P12.1) MUTATED   132  41
  DEL PEAK 45(20P12.1) WILD-TYPE 325  65
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                           173                            390 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                            41                             65 
$`DEL PEAK 45(20P12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5660 
       17.79        42.28        15.52        34.65        14.53        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 
       23.61        32.71        29.16        24.13        25.18        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A56B TCGA-AA-3496 TCGA-AA-3510 
       24.39        20.12        20.28        52.44         1.02        63.98 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       38.99         9.07        34.03        26.01        12.99         0.99 
TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3715 
       24.00        13.94        78.08         5.98        85.05         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3841 TCGA-AA-3848 
        0.99        35.05        25.02         1.02        36.95         0.99 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 
       32.05        31.07        53.00        24.03         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3994 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L 
       34.03         2.01        27.02        19.00        34.03        17.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01Z 
       42.02        32.02        12.00        31.00         1.02        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-6964 
        2.96        39.98        40.96        21.37         1.58         0.76 
TCGA-AD-6965 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        0.20        15.75        75.25         5.23        11.74         1.94 
TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
      102.44        21.99         2.01         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6169 
       22.03        30.08        16.01        29.03        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5540 
       15.02        11.01        11.08        11.01        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6929 
       11.51         1.32         7.92        15.12         7.53        13.41 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28A 
       92.75        49.91        13.32        44.32       131.51        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
      119.93        35.97         8.61        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6315 
        1.28         0.53        28.21         8.35        23.51        36.72 
TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A50V TCGA-AF-2689 TCGA-AF-3913 TCGA-AG-3574 
       26.43        46.75         5.06        17.95        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3593 
       32.02         7.07         1.02         2.01        24.00        34.03 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       50.04         6.05        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 
       29.98         0.99         1.02        32.02        36.03         1.02 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
        0.99        13.94        15.95         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6547 TCGA-AH-6643 
       70.03        64.01         1.94        38.96         1.45         0.69 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 
        4.73        60.03        10.98        12.00         7.10        30.05 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
       13.05        10.06        41.36        57.24        24.13        32.61 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        2.40        15.85        17.69        16.41        11.51        10.78 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6641 
        8.45        31.30        14.86         0.46        26.43 

$`DEL PEAK 45(20P12.1) 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-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.04        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       33.53        22.09        22.06        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.08        24.16        20.61        24.69        23.87        19.66 
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-3502 TCGA-AA-3506 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        58.03         6.97 
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-3532 TCGA-AA-3534 TCGA-AA-3544 
        8.05        19.07        19.07        29.00        29.00        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        13.02        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        19.99        61.02         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-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3833 
        5.03        26.99        19.04         0.99        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 
       38.99        37.02        14.93        17.03        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        17.03        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-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       24.00        21.99        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-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       13.94        38.04        30.02        18.05        18.05         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-A01D TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R 
       15.02        15.02         0.99        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        26.01        39.06        51.98 
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-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05         0.07         4.21        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        1.02         0.10         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-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.19         5.52        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-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        21.01 
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-5341 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       26.04        29.06        22.98        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       21.99        14.99        14.04        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 
       10.06        12.03        14.99        19.59        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       17.75        18.25        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-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D8 
        9.04         9.44        11.64        12.00       119.70        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       14.04        81.37        60.79       117.07        98.24        95.18 
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-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
        1.55        16.31        35.41        19.43       107.67        82.39 
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-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6321 
       51.75        45.11        39.42        35.93        36.00        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV 
       52.80         4.11         2.79         5.98         5.59        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       17.29        14.76        24.13        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        12.72        37.74        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3587 
       20.02        10.39        12.00         8.02         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3731 TCGA-AG-3732 
        2.01        12.03         0.99        19.99         1.02        32.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       14.01         1.02        48.03        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        20.98         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       36.03         9.07        10.98        51.98        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.04         0.49         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
       10.19         6.05         6.05         6.97         9.37        13.97 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
        7.99        11.01        15.02        12.99        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG 
       36.00        12.95         5.29       126.44       129.27        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.34        16.31         8.61        13.64        17.46        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        37.51         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76        18.28        55.76        47.08 

  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                        17.690                         18.015 
[1] "0.2 - 131.5 (17.7)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.5"
D72V2, continuous
D72V3, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED   121  60
  DEL PEAK 45(20P12.1) WILD-TYPE 308  99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED    121   60
  DEL PEAK 45(20P12.1) WILD-TYPE  308   99
        clus
vv       DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  COLON                           121                            308
  RECTUM                           60                             99
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 45(20P12.1) MUTATED        24        0       15        46         1
  DEL PEAK 45(20P12.1) WILD-TYPE      78        1       21       119         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(20P12.1) MUTATED           2         6          7         31
  DEL PEAK 45(20P12.1) WILD-TYPE         1        20         15         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 45(20P12.1) MUTATED           20       18         8         0
  DEL PEAK 45(20P12.1) WILD-TYPE         32       42        17         1
D72V4, multiclass
            clus
vv           DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  STAGE I                              24                             78
  STAGE IA                              0                              1
  STAGE II                             15                             21
  STAGE IIA                            46                            119
  STAGE IIB                             1                              9
  STAGE IIC                             2                              1
  STAGE III                             6                             20
  STAGE IIIA                            7                             15
  STAGE IIIB                           31                             45
  STAGE IIIC                           20                             32
  STAGE IV                             18                             42
  STAGE IVA                             8                             17
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 45(20P12.1) MUTATED       4  27 131  19
  DEL PEAK 45(20P12.1) WILD-TYPE    16  78 272  43
D72V5, multiclass
       clus
vv      DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  T0+T1                            4                             16
  T2                              27                             78
  T3                             131                            272
  T4                              19                             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 45(20P12.1) MUTATED    94  52  35
  DEL PEAK 45(20P12.1) WILD-TYPE 241  94  73
D72V6, multiclass
    clus
vv   DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  N0                           94                            241
  N1                           52                             94
  N2                           35                             73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 45(20P12.1) MUTATED   142  23   2   0  13
  DEL PEAK 45(20P12.1) WILD-TYPE 301  49   7   1  45
D72V7, multiclass
     clus
vv    DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  M0                           142                            301
  M1                            23                             49
  M1A                            2                              7
  M1B                            0                              1
  MX                            13                             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"
D72V8, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED    90  91
  DEL PEAK 45(20P12.1) WILD-TYPE 187 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED     90   91
  DEL PEAK 45(20P12.1) WILD-TYPE  187  224
        clus
vv       DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  FEMALE                           90                            187
  MALE                             91                            224
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 45(20P12.1) MUTATED                    108
  DEL PEAK 45(20P12.1) WILD-TYPE                  265
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(20P12.1) MUTATED                              13
  DEL PEAK 45(20P12.1) WILD-TYPE                            42
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 45(20P12.1) MUTATED                      55
  DEL PEAK 45(20P12.1) WILD-TYPE                    88
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(20P12.1) MUTATED                                5
  DEL PEAK 45(20P12.1) WILD-TYPE                              8
D72V9, multiclass
                                clus
vv                               DEL PEAK 45(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                    108
  COLON MUCINOUS ADENOCARCINOMA                            13
  RECTAL ADENOCARCINOMA                                    55
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 45(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      265
  COLON MUCINOUS ADENOCARCINOMA                              42
  RECTAL ADENOCARCINOMA                                      88
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED     0 181
  DEL PEAK 45(20P12.1) WILD-TYPE   9 402
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED      0  181
  DEL PEAK 45(20P12.1) WILD-TYPE    9  402
     clus
vv    DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  NO                             0                              9
  YES                          181                            402
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 45(20P12.1) MUTATED   130   1  11   4
  DEL PEAK 45(20P12.1) WILD-TYPE 296   4  25  23
D72V11, multiclass
    clus
vv   DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  R0                          130                            296
  R1                            1                              4
  R2                           11                             25
  RX                            4                             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"
D72V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 45(20P12.1) MUTATED                                  0     0
  DEL PEAK 45(20P12.1) WILD-TYPE                                1    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 45(20P12.1) MUTATED                           9    94
  DEL PEAK 45(20P12.1) WILD-TYPE                        35   198
D72V13, multiclass
                                  clus
vv                                 DEL PEAK 45(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      94
                                  clus
vv                                 DEL PEAK 45(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    35
  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(73) Variable = DEL PEAK 46(20P12.1) MUTATION ANALYSIS
D73V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 46(20P12.1) MUTATED   132  41
  DEL PEAK 46(20P12.1) WILD-TYPE 325  65
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                           173                            390 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                            41                             65 
$`DEL PEAK 46(20P12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2678 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-4105 TCGA-A6-5660 
       17.79        42.28        15.52        34.65        14.53        29.19 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 
       23.61        32.71        29.16        24.13        25.18        21.76 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6782 TCGA-A6-A56B TCGA-AA-3496 TCGA-AA-3510 
       24.39        20.12        20.28        52.44         1.02        63.98 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3531 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3543 
       38.99         9.07        34.03        26.01        12.99         0.99 
TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3697 TCGA-AA-3715 
       24.00        13.94        78.08         5.98        85.05         0.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3841 TCGA-AA-3848 
        0.99        35.05        25.02         1.02        36.95         0.99 
TCGA-AA-3855 TCGA-AA-3860 TCGA-AA-3864 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3955 
       32.05        31.07        53.00        24.03         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3994 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00L 
       34.03         2.01        27.02        19.00        34.03        17.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01Z 
       42.02        32.02        12.00        31.00         1.02        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A03J TCGA-AD-6548 TCGA-AD-6899 TCGA-AD-6964 
        2.96        39.98        40.96        21.37         1.58         0.76 
TCGA-AD-6965 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6608 
        0.20        15.75        75.25         5.23        11.74         1.94 
TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
      102.44        21.99         2.01         8.02        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6169 
       22.03        30.08        16.01        29.03        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5540 
       15.02        11.01        11.08        11.01        12.26        13.51 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6929 
       11.51         1.32         7.92        15.12         7.53        13.41 
TCGA-D5-6930 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        1.51        11.38        10.26        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28A 
       92.75        49.91        13.32        44.32       131.51        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
      119.93        35.97         8.61        29.59        16.24        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6294 TCGA-G4-6295 TCGA-G4-6298 TCGA-G4-6315 
        1.28         0.53        28.21         8.35        23.51        36.72 
TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A50V TCGA-AF-2689 TCGA-AF-3913 TCGA-AG-3574 
       26.43        46.75         5.06        17.95        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3593 
       32.02         7.07         1.02         2.01        24.00        34.03 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       50.04         6.05        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 
       29.98         0.99         1.02        32.02        36.03         1.02 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
        0.99        13.94        15.95         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6547 TCGA-AH-6643 
       70.03        64.01         1.94        38.96         1.45         0.69 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 
        4.73        60.03        10.98        12.00         7.10        30.05 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
       13.05        10.06        41.36        57.24        24.13        32.61 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        2.40        15.85        17.69        16.41        11.51        10.78 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6641 
        8.45        31.30        14.86         0.46        26.43 

$`DEL PEAK 46(20P12.1) 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-A6-2679 TCGA-A6-2680 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-2684 TCGA-A6-2685 
       44.91        35.11        45.60        13.94        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.04        36.53        32.45        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 
       33.53        22.09        22.06        27.09        22.52         8.38 
TCGA-A6-6142 TCGA-A6-6649 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6781 
       25.08        24.16        20.61        24.69        23.87        19.66 
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-3502 TCGA-AA-3506 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        58.03         6.97 
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-3532 TCGA-AA-3534 TCGA-AA-3544 
        8.05        19.07        19.07        29.00        29.00        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 
       33.99        21.01        13.02        17.95        29.95        23.01 
TCGA-AA-3558 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 
       20.98        19.99        19.99        61.02         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-3685 TCGA-AA-3688 TCGA-AA-3692 
       47.01        15.02        11.01        37.05        19.00        36.00 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3713 TCGA-AA-3818 TCGA-AA-3831 TCGA-AA-3833 
        5.03        26.99        19.04         0.99        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3844 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 
       38.99        37.02        14.93        17.03        33.07        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3870 TCGA-AA-3875 
        0.99        31.07        17.03        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-3968 TCGA-AA-3971 TCGA-AA-3972 TCGA-AA-3973 TCGA-AA-3975 
       24.00        21.99        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-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       13.94        38.04        30.02        18.05        18.05         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-A01D TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R 
       15.02        15.02         0.99        31.00        38.07        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A024 TCGA-AA-A029 
        1.02        33.04        35.01        26.01        39.06        51.98 
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-AD-5900 TCGA-AD-6888 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 
       18.05         0.07         4.21        56.55         0.79         0.72 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
        1.02         0.10         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-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
        5.19         5.52        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-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        21.01 
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-5341 TCGA-CM-5348 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       26.04        29.06        22.98        15.02         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
       15.02        17.03        15.02        12.00        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       21.99        14.99        14.04        12.95        13.05        11.08 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 
       10.06        12.03        14.99        19.59        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       17.75        18.25        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-D5-6931 TCGA-DM-A0X9 TCGA-DM-A1D8 
        9.04         9.44        11.64        12.00       119.70        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 
      140.38         7.50       135.65         7.76       139.17         6.12 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       14.04        81.37        60.79       117.07        98.24        95.18 
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-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
        1.55        16.31        35.41        19.43       107.67        82.39 
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-G4-6309 TCGA-G4-6310 TCGA-G4-6311 TCGA-G4-6314 TCGA-G4-6317 TCGA-G4-6321 
       51.75        45.11        39.42        35.93        36.00        22.09 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6627 
       26.04        13.78        35.80        26.17        91.79        47.15 
TCGA-G4-6628 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YV 
       52.80         4.11         2.79         5.98         5.59        26.99 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       17.29        14.76        24.13        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       19.10        12.72        37.74        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3587 
       20.02        10.39        12.00         8.02         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3731 TCGA-AG-3732 
        2.01        12.03         0.99        19.99         1.02        32.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       14.01         1.02        48.03        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       17.03        20.98         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       36.03         9.07        10.98        51.98        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.04         0.49         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
       10.19         6.05         6.05         6.97         9.37        13.97 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
        7.99        11.01        15.02        12.99        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG 
       36.00        12.95         5.29       126.44       129.27        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.34        16.31         8.61        13.64        17.46        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        37.51         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76        18.28        55.76        47.08 

  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                        131.51                         140.38 
  DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE 
                        17.690                         18.015 
[1] "0.2 - 131.5 (17.7)" "0.1 - 140.4 (18.0)"
[1] "hr=" "1.5"
D73V2, continuous
D73V3, binary
                                cls
clus                               0   1
  DEL PEAK 46(20P12.1) MUTATED   121  60
  DEL PEAK 46(20P12.1) WILD-TYPE 308  99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED    121   60
  DEL PEAK 46(20P12.1) WILD-TYPE  308   99
        clus
vv       DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  COLON                           121                            308
  RECTUM                           60                             99
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 46(20P12.1) MUTATED        24        0       15        46         1
  DEL PEAK 46(20P12.1) WILD-TYPE      78        1       21       119         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(20P12.1) MUTATED           2         6          7         31
  DEL PEAK 46(20P12.1) WILD-TYPE         1        20         15         45
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 46(20P12.1) MUTATED           20       18         8         0
  DEL PEAK 46(20P12.1) WILD-TYPE         32       42        17         1
D73V4, multiclass
            clus
vv           DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  STAGE I                              24                             78
  STAGE IA                              0                              1
  STAGE II                             15                             21
  STAGE IIA                            46                            119
  STAGE IIB                             1                              9
  STAGE IIC                             2                              1
  STAGE III                             6                             20
  STAGE IIIA                            7                             15
  STAGE IIIB                           31                             45
  STAGE IIIC                           20                             32
  STAGE IV                             18                             42
  STAGE IVA                             8                             17
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 46(20P12.1) MUTATED       4  27 131  19
  DEL PEAK 46(20P12.1) WILD-TYPE    16  78 272  43
D73V5, multiclass
       clus
vv      DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  T0+T1                            4                             16
  T2                              27                             78
  T3                             131                            272
  T4                              19                             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 46(20P12.1) MUTATED    94  52  35
  DEL PEAK 46(20P12.1) WILD-TYPE 241  94  73
D73V6, multiclass
    clus
vv   DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  N0                           94                            241
  N1                           52                             94
  N2                           35                             73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A M1B  MX
  DEL PEAK 46(20P12.1) MUTATED   142  23   2   0  13
  DEL PEAK 46(20P12.1) WILD-TYPE 301  49   7   1  45
D73V7, multiclass
     clus
vv    DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  M0                           142                            301
  M1                            23                             49
  M1A                            2                              7
  M1B                            0                              1
  MX                            13                             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"
D73V8, binary
                                cls
clus                               0   1
  DEL PEAK 46(20P12.1) MUTATED    90  91
  DEL PEAK 46(20P12.1) WILD-TYPE 187 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED     90   91
  DEL PEAK 46(20P12.1) WILD-TYPE  187  224
        clus
vv       DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  FEMALE                           90                            187
  MALE                             91                            224
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 46(20P12.1) MUTATED                    108
  DEL PEAK 46(20P12.1) WILD-TYPE                  265
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(20P12.1) MUTATED                              13
  DEL PEAK 46(20P12.1) WILD-TYPE                            42
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 46(20P12.1) MUTATED                      55
  DEL PEAK 46(20P12.1) WILD-TYPE                    88
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(20P12.1) MUTATED                                5
  DEL PEAK 46(20P12.1) WILD-TYPE                              8
D73V9, multiclass
                                clus
vv                               DEL PEAK 46(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                    108
  COLON MUCINOUS ADENOCARCINOMA                            13
  RECTAL ADENOCARCINOMA                                    55
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 46(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      265
  COLON MUCINOUS ADENOCARCINOMA                              42
  RECTAL ADENOCARCINOMA                                      88
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, binary
                                cls
clus                               0   1
  DEL PEAK 46(20P12.1) MUTATED     0 181
  DEL PEAK 46(20P12.1) WILD-TYPE   9 402
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(20P12.1) MUTATED      0  181
  DEL PEAK 46(20P12.1) WILD-TYPE    9  402
     clus
vv    DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  NO                             0                              9
  YES                          181                            402
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 46(20P12.1) MUTATED   130   1  11   4
  DEL PEAK 46(20P12.1) WILD-TYPE 296   4  25  23
D73V11, multiclass
    clus
vv   DEL PEAK 46(20P12.1) MUTATED DEL PEAK 46(20P12.1) WILD-TYPE
  R0                          130                            296
  R1                            1                              4
  R2                           11                             25
  RX                            4                             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"
D73V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 46(20P12.1) MUTATED                                  0     0
  DEL PEAK 46(20P12.1) WILD-TYPE                                1    12
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 46(20P12.1) MUTATED                           9    94
  DEL PEAK 46(20P12.1) WILD-TYPE                        35   198
D73V13, multiclass
                                  clus
vv                                 DEL PEAK 46(20P12.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      94
                                  clus
vv                                 DEL PEAK 46(20P12.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                        12
  BLACK OR AFRICAN AMERICAN                                    35
  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(74) Variable = DEL PEAK 47(21Q11.2) MUTATION ANALYSIS
D74V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 47(21Q11.2) MUTATED   158  38
  DEL PEAK 47(21Q11.2) WILD-TYPE 299  68
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                           196                            367 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                            38                             68 
$`DEL PEAK 47(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-QG-A5YV TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        4.11         5.98        26.99        24.13        17.95        17.23 
TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       19.10        14.50        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 
       12.00         7.07         1.02        24.00        46.03        34.03 
TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3728 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 
       12.03        19.99        29.98        19.99        17.03         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A01L 
       48.03        19.99        36.03        14.04        17.03        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       31.00        70.03        64.01        10.98         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6624 TCGA-CL-4957 
       61.97        41.00         0.49         0.69         4.73        13.97 
TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       10.98        13.97        36.00         7.10        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      126.44        57.24        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       20.55        20.91        15.85        17.69        16.34        16.41 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45        31.30         0.39         1.02         0.66 
TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
        0.53         0.76        18.28        26.43 

$`DEL PEAK 47(21Q11.2) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 TCGA-A6-2679 
        5.06        46.65        43.43        23.38        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-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 
       34.65        36.53        32.45        32.91        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       33.53        23.61        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6780 
        8.38        25.08        25.18        24.16        24.69        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 
       19.66        16.24        24.92        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-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3543 TCGA-AA-3548 
        8.05        29.00        29.00        12.99         0.99        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       21.01        24.00        17.95        29.95        20.98        13.94 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3662 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       19.99        61.02         6.05         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-3696 TCGA-AA-3697 TCGA-AA-3710 TCGA-AA-3713 
       11.01         5.98         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-3841 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 
       15.95        36.95        17.03        33.07        36.03        32.05 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3870 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3939 
       31.07        53.00        29.98        31.00         2.01        12.99 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3956 TCGA-AA-3971 
       33.01        26.01        24.00         2.01        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-A00N TCGA-AA-A00R TCGA-AA-A00U 
       34.03        18.05        18.05         4.01         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       14.99        34.98        15.02        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-A02E TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y 
       37.02        39.06         2.96         5.03        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-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-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        15.75         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-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-6606 TCGA-AZ-6608 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
      100.01        11.74         1.94         3.06         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-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.01         2.93       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5348 
       23.05        37.02         8.02        26.04        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       30.08        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        13.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        10.06        12.03 
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-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25         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-D5-6927 
       12.49        16.14        15.58         7.53        12.39         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-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB 
       38.20       130.65        92.75        12.59        44.32       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A285 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
        7.76       139.17         6.12        14.04        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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 
       11.11        13.64        13.45         6.18        16.31         1.28 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6294 TCGA-G4-6297 TCGA-G4-6298 TCGA-G4-6299 
       19.43       107.67        28.21        82.39        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-G4-6321 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6586 
       45.11        39.42        22.09        26.04        13.78        35.80 
TCGA-G4-6588 TCGA-G4-6627 TCGA-G4-6628 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB 
       26.17        47.15        52.80         5.06         2.79         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 
       17.29        14.76        43.04        13.55        12.72        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 
       10.39         8.45        32.02         8.02         2.01         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
        2.01        50.04         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99         1.02        32.98         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 
        1.02        36.95        13.02        35.01        14.01        32.02 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       28.04         1.02         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
        1.02        51.98        49.97        38.04         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
        9.37        60.03         7.99        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC 
       12.00        15.02        30.05        12.95         5.29        41.36 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 
      129.27        24.13        19.96        17.00        18.28        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 
        8.61        11.51        10.78        13.64        17.46         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 
       37.51        14.86         0.69         1.12         0.46        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                          0.20                           0.07 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                        140.38                         139.17 
  DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE 
                         17.13                          18.05 
[1] "0.2 - 140.4 (17.1)" "0.1 - 139.2 (18.1)"
[1] "hr=" "1.2"
D74V2, continuous
D74V3, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q11.2) MUTATED   134  69
  DEL PEAK 47(21Q11.2) WILD-TYPE 295  90
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED    134   69
  DEL PEAK 47(21Q11.2) WILD-TYPE  295   90
        clus
vv       DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  COLON                           134                            295
  RECTUM                           69                             90
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 47(21Q11.2) MUTATED        33        0       14        49         2
  DEL PEAK 47(21Q11.2) WILD-TYPE      69        1       22       116         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(21Q11.2) MUTATED           1         7         12         27
  DEL PEAK 47(21Q11.2) WILD-TYPE         2        19         10         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 47(21Q11.2) MUTATED           21       28         7         0
  DEL PEAK 47(21Q11.2) WILD-TYPE         31       32        18         1
D74V4, multiclass
            clus
vv           DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  STAGE I                              33                             69
  STAGE IA                              0                              1
  STAGE II                             14                             22
  STAGE IIA                            49                            116
  STAGE IIB                             2                              8
  STAGE IIC                             1                              2
  STAGE III                             7                             19
  STAGE IIIA                           12                             10
  STAGE IIIB                           27                             49
  STAGE IIIC                           21                             31
  STAGE IV                             28                             32
  STAGE IVA                             7                             18
  STAGE IVB                             0                              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                             T0+T1  T2  T3  T4
  DEL PEAK 47(21Q11.2) MUTATED       7  39 137  23
  DEL PEAK 47(21Q11.2) WILD-TYPE    13  66 266  39
D74V5, multiclass
       clus
vv      DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  T0+T1                            7                             13
  T2                              39                             66
  T3                             137                            266
  T4                              23                             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 47(21Q11.2) MUTATED   103  56  47
  DEL PEAK 47(21Q11.2) WILD-TYPE 232  90  61
D74V6, multiclass
    clus
vv   DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  N0                          103                            232
  N1                           56                             90
  N2                           47                             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 47(21Q11.2) MUTATED   147  30   3   0  25
  DEL PEAK 47(21Q11.2) WILD-TYPE 296  42   6   1  33
D74V7, multiclass
     clus
vv    DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  M0                           147                            296
  M1                            30                             42
  M1A                            3                              6
  M1B                            0                              1
  MX                            25                             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"
D74V8, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q11.2) MUTATED    93 113
  DEL PEAK 47(21Q11.2) WILD-TYPE 184 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED     93  113
  DEL PEAK 47(21Q11.2) WILD-TYPE  184  202
        clus
vv       DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  FEMALE                           93                            184
  MALE                            113                            202
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 47(21Q11.2) MUTATED                    125
  DEL PEAK 47(21Q11.2) WILD-TYPE                  248
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 47(21Q11.2) MUTATED                               8
  DEL PEAK 47(21Q11.2) WILD-TYPE                            47
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 47(21Q11.2) MUTATED                      64
  DEL PEAK 47(21Q11.2) WILD-TYPE                    79
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 47(21Q11.2) MUTATED                                3
  DEL PEAK 47(21Q11.2) WILD-TYPE                             10
D74V9, multiclass
                                clus
vv                               DEL PEAK 47(21Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    125
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    64
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 47(21Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      248
  COLON MUCINOUS ADENOCARCINOMA                              47
  RECTAL ADENOCARCINOMA                                      79
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q11.2) MUTATED     5 201
  DEL PEAK 47(21Q11.2) WILD-TYPE   4 382
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q11.2) MUTATED      5  201
  DEL PEAK 47(21Q11.2) WILD-TYPE    4  382
     clus
vv    DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  NO                             5                              4
  YES                          201                            382
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(21Q11.2) MUTATED   145   2  14   7
  DEL PEAK 47(21Q11.2) WILD-TYPE 281   3  22  20
D74V11, multiclass
    clus
vv   DEL PEAK 47(21Q11.2) MUTATED DEL PEAK 47(21Q11.2) WILD-TYPE
  R0                          145                            281
  R1                            2                              3
  R2                           14                             22
  RX                            7                             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"
D74V12, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 47(21Q11.2) MUTATED                                  1     4
  DEL PEAK 47(21Q11.2) WILD-TYPE                                0     8
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 47(21Q11.2) MUTATED                          14   105
  DEL PEAK 47(21Q11.2) WILD-TYPE                        30   187
D74V13, multiclass
                                  clus
vv                                 DEL PEAK 47(21Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  14
  WHITE                                                     105
                                  clus
vv                                 DEL PEAK 47(21Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         8
  BLACK OR AFRICAN AMERICAN                                    30
  WHITE                                                       187
[1] 4 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(75) Variable = DEL PEAK 48(22Q13.32) MUTATION ANALYSIS
D75V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 48(22Q13.32) MUTATED   161  44
  DEL PEAK 48(22Q13.32) WILD-TYPE 296  62
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            205                             358 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                             44                              62 
$`DEL PEAK 48(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-G4-6310 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6625 TCGA-G4-6626 TCGA-NH-A50T 
       45.11        36.72        36.00        91.79        46.75         4.11 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-QG-A5YV TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
        5.06         5.98        26.99        13.55        19.10        14.50 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       15.39        10.39        12.00        32.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3728 
        2.01        24.00        34.03        50.04        15.95        29.98 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 
        1.02        19.99         1.02         1.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A020 
       36.03        14.04        25.97        23.01        12.00        10.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6644 TCGA-BM-6198 
        1.94        38.96        41.00         0.49         0.72        10.19 
TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
        6.05         4.73        13.97        10.98        11.01        12.99 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC 
       13.97         7.10        30.05        13.05        10.06        41.36 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 
       51.48        32.61         2.40        20.55        17.69        16.31 
TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 
       16.41        14.86         0.39         0.66         0.76        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 48(22Q13.32) WILD-TYPE`
TCGA-3L-AA1B TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2677 
        5.06        46.65        43.76        43.43        23.38        17.79 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5661 
       37.05        37.25        16.04        32.45        32.91        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       22.09        22.06        32.71        29.16        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6649 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        24.16        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-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-3518 TCGA-AA-3524 
       58.03        63.98         1.02        13.02         1.02        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-3553 TCGA-AA-3554 TCGA-AA-3555 TCGA-AA-3556 TCGA-AA-3558 
       14.01        24.00        17.95        29.95        23.01        20.98 
TCGA-AA-3562 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       19.99        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3672 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3688 
        0.92        47.05        47.01        15.02        11.01        19.00 
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-3844 
        0.99        25.02         1.02        17.98        15.95        14.93 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       36.03        53.00        31.00        24.00        33.01        26.01 
TCGA-AA-3950 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
       24.00        20.98        34.03        16.08        34.06        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-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-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       34.98        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-A01V 
       31.00        38.07         1.02        35.01         1.02        35.01 
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-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6548 TCGA-AD-6888 
       22.03        39.98        18.05         0.07        21.37         4.21 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6895 TCGA-AD-6963 TCGA-AD-6964 TCGA-AM-5820 
       56.55         0.79         0.72         0.10         0.76         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09         0.95        21.44        17.82         5.19 
TCGA-AZ-4308 TCGA-AZ-4313 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4681 TCGA-AZ-4682 
       75.25        50.37        58.39        32.94        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-6606 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 
       11.74         2.14         3.25         3.29         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-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.01         2.93       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
       20.02        37.02        26.04        27.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       22.98        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-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-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 
       11.08        12.03        12.26        19.59        11.51        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       17.75        18.25         4.50        17.13        16.14        15.58 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        14.30         9.04         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-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       92.75        49.91         7.50       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
       14.04        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-F4-6854 
        6.18        35.87        16.31        29.59        33.67         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-G4-6320 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-A5IV TCGA-NH-A6GB 
       35.80        26.17        47.15        52.80         2.79         5.59 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       17.29        14.76        24.13        17.95        17.23        43.04 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 
       12.72        37.74        10.39         8.45        20.02        36.03 
TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
        8.02         1.02        46.03         2.01        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
        0.99        19.99        19.99         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       14.01        48.03        32.02         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       20.98        13.94         6.02        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        9.07         1.02        31.00        70.03        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       49.97        61.97        38.04         1.45         0.69         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        1.81         6.05         6.97         9.37        60.03         7.99 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 
       15.02        12.00        15.02        36.00        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6507 
      126.44        57.24       129.27        24.13         0.49        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6882 
       20.91        17.00        18.28        15.85        16.34         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
        9.96        37.51        31.30         1.02         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.46        55.76        47.08 

  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                           0.20                            0.07 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                         140.38                          139.17 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                          15.39                           19.07 
[1] "0.2 - 140.4 (15.4)" "0.1 - 139.2 (19.1)"
[1] "hr=" "1.5"
D75V2, continuous
D75V3, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED   150  65
  DEL PEAK 48(22Q13.32) WILD-TYPE 279  94
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED    150   65
  DEL PEAK 48(22Q13.32) WILD-TYPE  279   94
        clus
vv       DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  COLON                            150                             279
  RECTUM                            65                              94
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 48(22Q13.32) MUTATED        28        0        9        57         1
  DEL PEAK 48(22Q13.32) WILD-TYPE      74        1       27       108         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(22Q13.32) MUTATED           1        10         13         28
  DEL PEAK 48(22Q13.32) WILD-TYPE         2        16          9         48
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 48(22Q13.32) MUTATED           22       33        10         0
  DEL PEAK 48(22Q13.32) WILD-TYPE         30       27        15         1
D75V4, multiclass
            clus
vv           DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  STAGE I                               28                              74
  STAGE IA                               0                               1
  STAGE II                               9                              27
  STAGE IIA                             57                             108
  STAGE IIB                              1                               9
  STAGE IIC                              1                               2
  STAGE III                             10                              16
  STAGE IIIA                            13                               9
  STAGE IIIB                            28                              48
  STAGE IIIC                            22                              30
  STAGE IV                              33                              27
  STAGE IVA                             10                              15
  STAGE IVB                              0                               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                              T0+T1  T2  T3  T4
  DEL PEAK 48(22Q13.32) MUTATED       4  36 153  25
  DEL PEAK 48(22Q13.32) WILD-TYPE    16  69 250  37
D75V5, multiclass
       clus
vv      DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  T0+T1                             4                              16
  T2                               36                              69
  T3                              153                             250
  T4                               25                              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 48(22Q13.32) MUTATED   101  69  47
  DEL PEAK 48(22Q13.32) WILD-TYPE 234  77  61
D75V6, multiclass
    clus
vv   DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  N0                           101                             234
  N1                            69                              77
  N2                            47                              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 48(22Q13.32) MUTATED   150  39   3   0  22
  DEL PEAK 48(22Q13.32) WILD-TYPE 293  33   6   1  36
D75V7, multiclass
     clus
vv    DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  M0                            150                             293
  M1                             39                              33
  M1A                             3                               6
  M1B                             0                               1
  MX                             22                              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"
D75V8, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED    97 121
  DEL PEAK 48(22Q13.32) WILD-TYPE 180 194
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED     97  121
  DEL PEAK 48(22Q13.32) WILD-TYPE  180  194
        clus
vv       DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  FEMALE                            97                             180
  MALE                             121                             194
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                    141
  DEL PEAK 48(22Q13.32) WILD-TYPE                  232
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                               9
  DEL PEAK 48(22Q13.32) WILD-TYPE                            46
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                      61
  DEL PEAK 48(22Q13.32) WILD-TYPE                    82
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                                4
  DEL PEAK 48(22Q13.32) WILD-TYPE                              9
D75V9, multiclass
                                clus
vv                               DEL PEAK 48(22Q13.32) MUTATED
  COLON ADENOCARCINOMA                                     141
  COLON MUCINOUS ADENOCARCINOMA                              9
  RECTAL ADENOCARCINOMA                                     61
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               DEL PEAK 48(22Q13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                       232
  COLON MUCINOUS ADENOCARCINOMA                               46
  RECTAL ADENOCARCINOMA                                       82
  RECTAL MUCINOUS ADENOCARCINOMA                               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"
D75V10, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED     4 214
  DEL PEAK 48(22Q13.32) WILD-TYPE   5 369
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED      4  214
  DEL PEAK 48(22Q13.32) WILD-TYPE    5  369
     clus
vv    DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  NO                              4                               5
  YES                           214                             369
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 48(22Q13.32) MUTATED   148   2  17  11
  DEL PEAK 48(22Q13.32) WILD-TYPE 278   3  19  16
D75V11, multiclass
    clus
vv   DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  R0                           148                             278
  R1                             2                               3
  R2                            17                              19
  RX                            11                              16
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V12, continuous
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 48(22Q13.32) MUTATED                                  1     4
  DEL PEAK 48(22Q13.32) WILD-TYPE                                0     8
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 48(22Q13.32) MUTATED                          17   101
  DEL PEAK 48(22Q13.32) WILD-TYPE                        27   191
D75V13, multiclass
                                  clus
vv                                 DEL PEAK 48(22Q13.32) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   17
  WHITE                                                      101
                                  clus
vv                                 DEL PEAK 48(22Q13.32) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          8
  BLACK OR AFRICAN AMERICAN                                     27
  WHITE                                                        191
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
