[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/22506534/COADREAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/COADREAD-TP/22524544/transformed.cor.cli.txt"

nPatients in clinical file=629, in cluster file=616, common to both=614
[1]  72 614
[1] "AMP PEAK  1(1Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          145                           469 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          145                           469 
[1] "AMP PEAK  2(2Q33.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          140                           474 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          140                           474 
[1] "AMP PEAK  3(5P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        116                         498 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        116                         498 
[1] "AMP PEAK  4(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                          154                           460 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                          154                           460 
[1] "AMP PEAK  5(7P21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE 
                          361                           253 
  AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE 
                          361                           253 
[1] "AMP PEAK  6(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           210                            404 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           210                            404 
[1] "AMP PEAK  7(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           254                            360 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           254                            360 
[1] "AMP PEAK  8(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                           366                            248 
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                           366                            248 
[1] "AMP PEAK  9(10Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE 
                            40                            574 
  AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE 
                            40                            574 
[1] "AMP PEAK 10(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                           136                            478 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                           136                            478 
[1] "AMP PEAK 11(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                            153                             461 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                            153                             461 
[1] "AMP PEAK 12(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            401                             213 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            401                             213 
[1] "AMP PEAK 13(13Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                           395                            219 
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                           395                            219 
[1] "AMP PEAK 14(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                           397                            217 
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                           397                            217 
[1] "AMP PEAK 15(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE 
                            42                            572 
  AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE 
                            42                            572 
[1] "AMP PEAK 16(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE 
                           172                            442 
  AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE 
                           172                            442 
[1] "AMP PEAK 17(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                         160                          454 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                         160                          454 
[1] "AMP PEAK 18(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                           144                            470 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                           144                            470 
[1] "AMP PEAK 19(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE 
                         139                          475 
  AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE 
                         139                          475 
[1] "AMP PEAK 20(20P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE 
                           278                            336 
  AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE 
                           278                            336 
[1] "AMP PEAK 21(20P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE 
                            362                             252 
  AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE 
                            362                             252 
[1] "AMP PEAK 22(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                            467                             147 
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                            467                             147 
[1] "AMP PEAK 23(20Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE 
                         469                          145 
  AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE 
                         469                          145 
[1] "AMP PEAK 24(20Q13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE 
                            471                             143 
  AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE 
                            471                             143 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           243                            371 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           243                            371 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        176                         438 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        176                         438 
[1] "DEL PEAK  3(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          175                           439 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          175                           439 
[1] "DEL PEAK  4(2P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         593 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         593 
[1] "DEL PEAK  5(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           35                           579 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           35                           579 
[1] "DEL PEAK  6(3P26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           92                           522 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           92                           522 
[1] "DEL PEAK  7(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          118                           496 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          118                           496 
[1] "DEL PEAK  8(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            64                            550 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            64                            550 
[1] "DEL PEAK  9(4P16.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE 
                          201                           413 
  DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE 
                          201                           413 
[1] "DEL PEAK 10(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          223                           391 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          223                           391 
[1] "DEL PEAK 11(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          231                           383 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          231                           383 
[1] "DEL PEAK 12(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          158                           456 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          158                           456 
[1] "DEL PEAK 13(5Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          186                           428 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          186                           428 
[1] "DEL PEAK 14(5Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          188                           426 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          188                           426 
[1] "DEL PEAK 15(5Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE 
                          160                           454 
  DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE 
                          160                           454 
[1] "DEL PEAK 16(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           79                           535 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           79                           535 
[1] "DEL PEAK 17(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         91                         523 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         91                         523 
[1] "DEL PEAK 18(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           17                           597 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           17                           597 
[1] "DEL PEAK 19(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                          288                           326 
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                          288                           326 
[1] "DEL PEAK 20(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        302                         312 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        302                         312 
[1] "DEL PEAK 21(8Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           47                           567 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           47                           567 
[1] "DEL PEAK 22(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           87                           527 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           87                           527 
[1] "DEL PEAK 23(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                           113                            501 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                           113                            501 
[1] "DEL PEAK 24(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                           138                            476 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                           138                            476 
[1] "DEL PEAK 25(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            160                             454 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            160                             454 
[1] "DEL PEAK 26(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           156                            458 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           156                            458 
[1] "DEL PEAK 27(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE 
                           110                            504 
  DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE 
                           110                            504 
[1] "DEL PEAK 28(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE 
                            92                            522 
  DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE 
                            92                            522 
[1] "DEL PEAK 29(12Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE 
                             90                             524 
  DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE 
                             90                             524 
[1] "DEL PEAK 30(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE 
                           210                            404 
  DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE 
                           210                            404 
[1] "DEL PEAK 31(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                           218                            396 
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                           218                            396 
[1] "DEL PEAK 32(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                           248                            366 
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                           248                            366 
[1] "DEL PEAK 33(15Q15.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                           250                            364 
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                           250                            364 
[1] "DEL PEAK 34(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                           247                            367 
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                           247                            367 
[1] "DEL PEAK 35(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                            237                             377 
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                            237                             377 
[1] "DEL PEAK 36(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            68                            546 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            68                            546 
[1] "DEL PEAK 37(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            83                            531 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            83                            531 
[1] "DEL PEAK 38(17P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                         368                          246 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                         368                          246 
[1] "DEL PEAK 39(17Q24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                            95                            519 
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                            95                            519 
[1] "DEL PEAK 40(18P11.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                            369                             245 
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                            369                             245 
[1] "DEL PEAK 41(18Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           414                            200 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           414                            200 
[1] "DEL PEAK 42(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           431                            183 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           431                            183 
[1] "DEL PEAK 43(18Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                           426                            188 
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                           426                            188 
[1] "DEL PEAK 44(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            97                            517 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            97                            517 
[1] "DEL PEAK 45(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                           135                            479 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                           135                            479 
[1] "DEL PEAK 46(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           213                            401 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           213                            401 
[1] "DEL PEAK 47(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE 
                           209                            405 
  DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE 
                           209                            405 
[1] "DEL PEAK 48(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            226                             388 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            226                             388 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "TUMOR_STAGE"                         
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "ETHNICITY"                           

Input Data has 18 rows and 614 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=111,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=311,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=13,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'TUMOR_STAGE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=27,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 614 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "TUMOR_TISSUE_SITE"     "PATHOLOGIC_STAGE"     
 [4] "PATHOLOGY_T_STAGE"     "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"    
 [7] "GENDER"                "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"    
[10] "RESIDUAL_TUMOR"        "NUMBER_OF_LYMPH_NODES" "ETHNICITY"            
YEARS_TO_BIRTH, nv=59, binary=FALSE, numeric=TRUE
TUMOR_TISSUE_SITE, nv=2, binary=FALSE, numeric=FALSE
PATHOLOGIC_STAGE, nv=13, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 20 105 417  69 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 20 105 417  69 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 20 105 417  69 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 20 105 417  69 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
346 150 115 
[1] "table(vv)"
vv
 N0  N1  N2 
346 150 115 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
346 150 115 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
346 150 115 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=4, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=27, binary=FALSE, numeric=TRUE
ETHNICITY, nv=2, 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  37
  AMP PEAK  1(1Q31.1) WILD-TYPE 361  91
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          142                           452 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                           37                            91 
$`AMP PEAK  1(1Q31.1) MUTATED`
TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3688 TCGA-AA-3939 TCGA-AD-6888 TCGA-CK-5912 
       45.60        24.16        19.00        12.99        15.52        49.08 
TCGA-AG-3611 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       13.94        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6641 TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2679 
       26.43        12.66        39.45        43.76        43.76        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-6652 
       35.11        16.57        36.53        32.45        29.19        24.69 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3561 TCGA-AA-3660 
       23.87        56.25         5.03        38.99        13.94        78.08 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3696 
       54.02         2.01        47.05        47.01        15.02         5.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       10.06        33.07        32.05        31.07        17.03        27.02 
TCGA-AA-3947 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3994 TCGA-AA-A01D TCGA-AA-A01F 
       33.01        21.99        13.05        27.02        10.98        32.02 
TCGA-AA-A01R TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02Y TCGA-AD-6901 TCGA-AU-3779 
       35.01        26.01         2.96        39.98        22.42        14.50 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 
        0.20        17.85         5.65        22.36        65.00        12.10 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CM-4746 TCGA-CM-4747 
       11.74        12.69        12.36        12.20        37.02        25.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 
       22.98        30.08        15.02         5.03        15.02        14.04 
TCGA-CM-6167 TCGA-D5-5539 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 
       14.99        19.59        25.48        15.12        17.85        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-DM-A0X9 TCGA-DM-A1D4 
        7.53        10.13        12.43        14.30       119.70        92.75 
TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       81.37        35.97        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6311 
       11.11        47.41        82.39        74.56        65.85        39.42 
TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 
       18.18         9.93        42.77        21.90        38.70        46.92 
TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 
       13.55        29.98        24.36        24.59        32.02        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3881 TCGA-AG-3882 
       34.03        34.03         6.05        19.99        19.04        19.99 
TCGA-AG-3999 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       28.04        23.01        37.02         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 
       38.56        43.20        27.55        13.78        47.44        48.20 
TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
       25.05        13.97        31.00       129.27        24.13        32.61 
TCGA-EI-6506 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 
       20.55         8.61        10.78        13.64        11.97         9.96 
TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
        0.39        19.66        11.87        47.08 

$`AMP PEAK  1(1Q31.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        14.53         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        36.00        85.05        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       39.06        21.37        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
      100.01         1.94         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       17.85        10.39         8.02        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 
       25.97        15.95        55.76        15.62         4.80         1.61 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 
        9.53        46.65        43.43        42.90        42.28        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        34.65        32.75        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-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        20.61        21.76        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 
       20.28        16.24        24.92        61.84         9.63         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3667 
       24.00        29.95        20.98        61.02         6.97        14.01 
TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3710 TCGA-AA-3811 
       50.04        11.01         5.98        37.05        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       35.05         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       38.99        36.95        37.02         0.00        17.03         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 
        0.00        36.03         0.99        53.00        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        26.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       16.08        34.06        25.02        27.02         7.96        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-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-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       34.98        15.02        15.02        12.00        31.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
       38.07         1.02         1.02        33.04         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       41.00        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
        5.79        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94         5.13        62.79        88.21        49.41         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       29.56         5.23         3.19        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 
       82.95         2.01       124.27        23.05        20.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5860 
        8.02        27.02        13.02        29.06        22.03        32.02 
TCGA-CM-5863 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-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 
       21.99        12.99        13.02        15.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-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-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        45.40        54.61        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 
       20.42        17.75        18.25        43.27         4.80        17.13 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       16.14        15.58        12.39         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD 
       13.41        13.35        12.00        11.38        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        49.91        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-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6463 
       14.04        26.47       119.93        60.79       117.07        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       43.04        33.67        13.25         0.53        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
        8.35        67.30        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       74.79        10.98        19.33        19.33        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO 
       16.80        29.46        32.98         8.42        31.30        60.13 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       11.90        70.03        39.48        17.23        43.04        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       34.49        37.74        16.83        20.02        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.84        36.03        12.00         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 
       37.02        32.98         0.99         0.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A016 
        3.98        46.03        20.98        13.94         6.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
        1.02         1.02        49.97        61.97        41.00         2.50 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
       26.43        19.46         6.05        33.17        44.78        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
        7.17        21.01        26.04        31.00        12.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
      126.44        41.36        57.24        51.48         3.48         4.18 
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-6917 TCGA-EI-7004 
       16.34        16.31        16.41        11.51        17.46         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       49.51        42.35        28.57        32.19        36.49        37.18 
TCGA-F5-6861 TCGA-F5-6864 
       38.14        12.46 

  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                          0.2                           0.0 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                       129.27                        148.01 
  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE 
                       24.475                        21.010 
[1] "0.2 - 129.3 (24.5)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.2"
D1V2, continuous
D1V3, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED    96  47
  AMP PEAK  1(1Q31.1) WILD-TYPE 352 115
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     96   47
  AMP PEAK  1(1Q31.1) WILD-TYPE  352  115
        clus
vv       AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  COLON                           96                           352
  RECTUM                          47                           115
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  1(1Q31.1) MUTATED        18        0        7        35         2
  AMP PEAK  1(1Q31.1) WILD-TYPE      86        1       30       137        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  1(1Q31.1) MUTATED           0         5          6         18
  AMP PEAK  1(1Q31.1) WILD-TYPE         2        19          9         66
                               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         38       42        16         2
D1V4, multiclass
            clus
vv           AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  STAGE I                             18                            86
  STAGE IA                             0                             1
  STAGE II                             7                            30
  STAGE IIA                           35                           137
  STAGE IIB                            2                            10
  STAGE IIC                            0                             2
  STAGE III                            5                            19
  STAGE IIIA                           6                             9
  STAGE IIIB                          18                            66
  STAGE IIIC                          17                            38
  STAGE IV                            21                            42
  STAGE IVA                            8                            16
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  1(1Q31.1) MUTATED     4  21  97  21
  AMP PEAK  1(1Q31.1) WILD-TYPE  16  84 320  48
D1V5, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  T1                           4                            16
  T2                          21                            84
  T3                          97                           320
  T4                          21                            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
  AMP PEAK  1(1Q31.1) MUTATED    69  39  34
  AMP PEAK  1(1Q31.1) WILD-TYPE 277 111  81
D1V6, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  N0                          69                           277
  N1                          39                           111
  N2                          34                            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"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED    96  28
  AMP PEAK  1(1Q31.1) WILD-TYPE 357  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     96   28
  AMP PEAK  1(1Q31.1) WILD-TYPE  357   60
   clus
vv  AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  0                          96                           357
  1                          28                            60
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED    61  84
  AMP PEAK  1(1Q31.1) WILD-TYPE 228 241
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED     61   84
  AMP PEAK  1(1Q31.1) WILD-TYPE  228  241
        clus
vv       AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  FEMALE                          61                           228
  MALE                            84                           241
[1] 2 2
[1] FALSE
D1V9, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED   114  10
  AMP PEAK  1(1Q31.1) WILD-TYPE 368  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED    114   10
  AMP PEAK  1(1Q31.1) WILD-TYPE  368   19
     clus
vv    AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  NO                          114                           368
  YES                          10                            19
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                     87
  AMP PEAK  1(1Q31.1) WILD-TYPE                  295
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                               9
  AMP PEAK  1(1Q31.1) WILD-TYPE                            53
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                      43
  AMP PEAK  1(1Q31.1) WILD-TYPE                   103
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  1(1Q31.1) MUTATED                                3
  AMP PEAK  1(1Q31.1) WILD-TYPE                             10
D1V10, multiclass
                                clus
vv                               AMP PEAK  1(1Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    87
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   43
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               AMP PEAK  1(1Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     295
  COLON MUCINOUS ADENOCARCINOMA                             53
  RECTAL ADENOCARCINOMA                                    103
  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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  1(1Q31.1) MUTATED   100   1  11   6
  AMP PEAK  1(1Q31.1) WILD-TYPE 346   5  26  23
D1V11, multiclass
    clus
vv   AMP PEAK  1(1Q31.1) MUTATED AMP PEAK  1(1Q31.1) WILD-TYPE
  R0                         100                           346
  R1                           1                             5
  R2                          11                            26
  RX                           6                            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"
D1V12, continuous
D1V13, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q31.1) MUTATED     1  90
  AMP PEAK  1(1Q31.1) WILD-TYPE   4 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q31.1) MUTATED      1   90
  AMP PEAK  1(1Q31.1) WILD-TYPE    4  262
                        clus
vv                       AMP PEAK  1(1Q31.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          90
                        clus
vv                       AMP PEAK  1(1Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           262
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(2Q33.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(2Q33.1) MUTATED    99  34
  AMP PEAK  2(2Q33.1) WILD-TYPE 367  94
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                          133                           461 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                           34                            94 
$`AMP PEAK  2(2Q33.1) MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3562 TCGA-AA-3867 
       14.53        24.16         1.02        34.03        19.99        24.03 
TCGA-AA-3979 TCGA-AD-6548 TCGA-AD-6888 TCGA-G4-6310 TCGA-G4-6628 TCGA-NH-A8F7 
       24.00        21.37        15.52        63.62        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3890 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 TCGA-3L-AA1B 
       10.39        17.03        31.00        21.24        18.28        15.62 
TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
        1.61        39.45        43.76        34.65        36.53        32.91 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-A566 
       30.44        32.71        29.16        24.69        23.87        24.92 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 
       29.00        29.00        50.04        15.02        37.05         5.03 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3971 TCGA-AA-A00W 
       10.06        35.05        33.07         0.00        16.08        14.99 
TCGA-AA-A01I TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 
       31.00         1.02        26.01         2.96         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A8YK 
       27.42        26.47        16.44        16.31         0.20        18.84 
TCGA-AZ-4616 TCGA-AZ-6607 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-4950 TCGA-CK-5914 
        5.13         3.19        12.59        12.20        85.45        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        45.40        55.92         4.80 
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-G4-6311 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX 
       39.42        74.79        18.18        12.79        29.46        32.98 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-5654 
       38.70        60.13        46.92        39.48        17.23        16.83 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3591 
       24.36        86.63        65.98        36.03        46.03        34.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 
        6.05        19.99        19.99         1.02         1.02        48.03 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       28.04         1.02        46.03        38.04        38.56        43.20 
TCGA-AH-6897 TCGA-CI-6621 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6154 
       26.43        13.78        78.12         7.17        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6508 
       31.00        51.98        25.05       129.27         4.18        20.91 
TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6863 TCGA-F5-6864 
       16.31        13.64         9.96        49.51        11.87        12.46 
TCGA-G5-6572 
       47.08 

$`AMP PEAK  2(2Q33.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        13.94        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3552 
       37.05        36.03         8.05        19.07         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        23.01        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 
       19.07        38.04        21.99        39.06        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        23.51        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H 
       91.79         8.02        13.94        19.99        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 TCGA-4N-A93T 
       15.95        36.03        51.98        55.76        26.43         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       12.66         9.53        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       37.02        32.75        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        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        9.07        19.07         0.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3818 
       47.05        47.01        11.01         5.98        26.99         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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 
       37.02         0.00        17.03        10.06         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 
       20.98        34.03         2.01        21.99        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         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-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A017 
       27.02        42.02         0.99        17.03        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        32.02        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01        33.04         1.02        37.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
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        33.01 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       21.44        17.82        17.26        17.85        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41         5.65        32.94        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
        5.23        11.74        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.76        10.06        14.30        17.56       148.01 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       70.16        15.62        51.32        21.14        82.95         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        25.02        26.04 
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        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 
       15.02        15.02        15.02        12.00        16.04        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-D5-5538 
       11.08        11.08        11.01        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 
       25.48        43.27        15.12        17.85        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        13.35        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 
       10.26       119.70        38.20       130.65        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
      139.17        81.37       119.93        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6302 
        0.53        47.41        35.31       133.18        82.39        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       65.85        53.62        44.68        55.04        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50U 
       36.00        26.43        26.04        13.78        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 
        8.42        31.30        21.90        11.90        70.03        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6655 
       13.55        37.97        34.49        37.74        29.98        20.02 
TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       24.59        11.84        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.04        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 
       25.02        32.02        19.99        36.03        14.04         3.98 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       41.00         2.50        27.55        19.46         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       44.78        47.44        48.20        21.01        25.05        26.04 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       13.97        10.98        44.02        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        3.48        20.55        19.96        17.00        18.28        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-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.46        11.97         8.45        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       32.19        36.49        19.66        37.18        38.14 

  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                            0                             0 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                       129.27                        148.01 
  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE 
                        22.42                         21.99 
[1] "0.0 - 129.3 (22.4)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D2V2, continuous
D2V3, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    92  48
  AMP PEAK  2(2Q33.1) WILD-TYPE 356 114
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     92   48
  AMP PEAK  2(2Q33.1) WILD-TYPE  356  114
        clus
vv       AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  COLON                           92                           356
  RECTUM                          48                           114
[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        29         1
  AMP PEAK  2(2Q33.1) WILD-TYPE      83        1       29       143        11
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  2(2Q33.1) MUTATED           1         5          2         23
  AMP PEAK  2(2Q33.1) WILD-TYPE         1        19         13         61
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  2(2Q33.1) MUTATED           22       15         6         1
  AMP PEAK  2(2Q33.1) WILD-TYPE         33       48        18         1
D2V4, multiclass
            clus
vv           AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  STAGE I                             21                            83
  STAGE IA                             0                             1
  STAGE II                             8                            29
  STAGE IIA                           29                           143
  STAGE IIB                            1                            11
  STAGE IIC                            1                             1
  STAGE III                            5                            19
  STAGE IIIA                           2                            13
  STAGE IIIB                          23                            61
  STAGE IIIC                          22                            33
  STAGE IV                            15                            48
  STAGE IVA                            6                            18
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  2(2Q33.1) MUTATED     3  22  99  15
  AMP PEAK  2(2Q33.1) WILD-TYPE  17  83 318  54
D2V5, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  T1                           3                            17
  T2                          22                            83
  T3                          99                           318
  T4                          15                            54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  2(2Q33.1) MUTATED    64  34  41
  AMP PEAK  2(2Q33.1) WILD-TYPE 282 116  74
D2V6, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  N0                          64                           282
  N1                          34                           116
  N2                          41                            74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    94  23
  AMP PEAK  2(2Q33.1) WILD-TYPE 359  65
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     94   23
  AMP PEAK  2(2Q33.1) WILD-TYPE  359   65
   clus
vv  AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  0                          94                           359
  1                          23                            65
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED    67  73
  AMP PEAK  2(2Q33.1) WILD-TYPE 222 252
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED     67   73
  AMP PEAK  2(2Q33.1) WILD-TYPE  222  252
        clus
vv       AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  FEMALE                          67                           222
  MALE                            73                           252
[1] 2 2
[1] FALSE
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED   107   9
  AMP PEAK  2(2Q33.1) WILD-TYPE 375  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED    107    9
  AMP PEAK  2(2Q33.1) WILD-TYPE  375   20
     clus
vv    AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  NO                          107                           375
  YES                           9                            20
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                     81
  AMP PEAK  2(2Q33.1) WILD-TYPE                  301
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                              11
  AMP PEAK  2(2Q33.1) WILD-TYPE                            51
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                      48
  AMP PEAK  2(2Q33.1) WILD-TYPE                    98
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  2(2Q33.1) MUTATED                                0
  AMP PEAK  2(2Q33.1) WILD-TYPE                             13
D2V10, multiclass
                                clus
vv                               AMP PEAK  2(2Q33.1) MUTATED
  COLON ADENOCARCINOMA                                    81
  COLON MUCINOUS ADENOCARCINOMA                           11
  RECTAL ADENOCARCINOMA                                   48
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               AMP PEAK  2(2Q33.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     301
  COLON MUCINOUS ADENOCARCINOMA                             51
  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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  2(2Q33.1) MUTATED    96   3   8   9
  AMP PEAK  2(2Q33.1) WILD-TYPE 350   3  29  20
D2V11, multiclass
    clus
vv   AMP PEAK  2(2Q33.1) MUTATED AMP PEAK  2(2Q33.1) WILD-TYPE
  R0                          96                           350
  R1                           3                             3
  R2                           8                            29
  RX                           9                            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"
D2V12, continuous
D2V13, binary
                               cls
clus                              0   1
  AMP PEAK  2(2Q33.1) MUTATED     3  90
  AMP PEAK  2(2Q33.1) WILD-TYPE   2 262
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2Q33.1) MUTATED      3   90
  AMP PEAK  2(2Q33.1) WILD-TYPE    2  262
                        clus
vv                       AMP PEAK  2(2Q33.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          90
                        clus
vv                       AMP PEAK  2(2Q33.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           262
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(5P12) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  3(5P12) MUTATED    83  30
  AMP PEAK  3(5P12) WILD-TYPE 383  98
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        113                         481 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                         30                          98 
$`AMP PEAK  3(5P12) MUTATED`
TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3688 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 
       45.60        13.02        19.00        19.04        14.93        24.03 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00Z TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       50.99        26.01        21.99         1.94        49.08         5.88 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-3L-AA1B 
       17.03        17.03        25.97        36.03        31.00        15.62 
TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2685 TCGA-A6-4107 
        1.61        43.76        43.43        44.91        37.25        32.45 
TCGA-A6-6650 TCGA-AA-3488 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3666 
       20.61         5.03        26.01        12.99        24.00         2.01 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3854 TCGA-AA-3856 
       47.01         5.98        37.05        37.02        36.03         0.99 
TCGA-AA-3866 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A01D TCGA-AA-A029 TCGA-AA-A02E 
       17.03        21.99        34.03        10.98        51.98         2.96 
TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5821 
        2.01        41.00        40.96         5.79        16.44         0.92 
TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4614 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6603 
        0.20        18.84         5.65        62.79        49.41        29.56 
TCGA-CA-5254 TCGA-CM-4747 TCGA-CM-5860 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 
       12.69        25.02        32.02        15.02        14.04        29.03 
TCGA-CM-6167 TCGA-CM-6169 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-6531 TCGA-D5-6538 
       14.99        13.02        11.01        19.59        17.75        17.13 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A28M 
       14.30        13.41        11.38        12.59         7.50        95.18 
TCGA-F4-6460 TCGA-F4-6855 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A6GC TCGA-QG-A5Z1 
       31.96        47.41        46.75        74.79        12.79         8.42 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       38.70        46.92        37.74        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3609 TCGA-AG-3731 
       65.98        36.03        46.03        34.03        19.99        37.02 
TCGA-AG-3885 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A026 TCGA-AG-A02G 
       17.95        28.04        36.03         1.02         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-5869 TCGA-DC-6156 
       41.00        38.04        43.20        27.55        31.00        31.00 
TCGA-DC-6158 TCGA-DC-6683 TCGA-DY-A1DD TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 
       10.98        25.05        57.24         4.18        16.31        11.51 
TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 
        9.96        28.57        32.19        37.18        11.87 

$`AMP PEAK  3(5P12) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       34.03         0.99        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 
        6.05         0.92        36.00        85.05        19.04        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3979 TCGA-AA-3986 
       29.98        12.99        24.00         2.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       38.04        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
       75.95       106.75       100.01        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A014 
       17.85        10.39         8.02        13.94        19.99        15.95 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-4N-A93T 
       51.98        21.24        18.28        55.76        26.43         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 
       12.66         9.53        39.45        43.76        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 
       42.28        35.11        16.57        37.05        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        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-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
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        56.25         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
        0.00        29.00        29.00        14.01        33.99        21.01 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
       54.02        14.01        50.04        47.05        15.02        11.01 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 
        1.02        17.98        15.95        38.99        36.95         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 
       17.03        10.06         0.00        33.07         0.00        32.05 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       31.07        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 
       16.08        13.05        34.06        25.02        27.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02J 
       33.04         1.02        26.01        37.02        39.98         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
        0.92        22.03        39.98        18.05        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AU-3779 
       24.53        22.42        27.42        26.47         0.46        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        17.85        19.33       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6599 
       32.94         5.13        22.36        65.00        88.21         6.77 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 
       12.10         5.23        11.74         3.19        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4751 
       23.05        20.02        37.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 
        5.03        15.02        15.02        17.03        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        12.99        15.02        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       54.61        56.09        55.92        20.19        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6539 
       25.48        43.27        15.12        17.85         4.80        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        13.35        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-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
       13.32       140.38        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
       60.79       117.07        98.24         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       43.04        33.67        13.25         0.53        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.43        26.04        13.78        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       32.98        31.30        21.90        60.13        11.90        70.03 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       29.98        16.83        24.36        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 
       32.02         7.07        20.05        24.00         1.02        34.03 
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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       15.95        20.98         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        0.99         0.99        19.04        19.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       32.02        19.99        14.04         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 
        1.02        49.97        61.97        38.56         2.50        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       12.00        13.97        51.98        44.02        25.97        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
       12.62       126.44        41.36       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         3.48        20.55        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-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       10.78        13.64        17.46        11.97         8.45        49.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
       42.35         0.39        36.49        19.66        38.14        12.46 
TCGA-G5-6572 
       47.08 

  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                        0.2                         0.0 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                      95.18                      148.01 
  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE 
                      24.03                       21.99 
[1] "0.2 - 95.2 (24.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D3V2, continuous
D3V3, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    76  40
  AMP PEAK  3(5P12) WILD-TYPE 372 122
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     76   40
  AMP PEAK  3(5P12) WILD-TYPE  372  122
        clus
vv       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  COLON                         76                         372
  RECTUM                        40                         122
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  3(5P12) MUTATED        17        0        6        27         1
  AMP PEAK  3(5P12) WILD-TYPE      87        1       31       145        11
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  3(5P12) MUTATED           1         3          5         12
  AMP PEAK  3(5P12) WILD-TYPE         1        21         10         72
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  3(5P12) MUTATED           16       18         6         1
  AMP PEAK  3(5P12) WILD-TYPE         39       45        18         1
D3V4, multiclass
            clus
vv           AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  STAGE I                           17                          87
  STAGE IA                           0                           1
  STAGE II                           6                          31
  STAGE IIA                         27                         145
  STAGE IIB                          1                          11
  STAGE IIC                          1                           1
  STAGE III                          3                          21
  STAGE IIIA                         5                          10
  STAGE IIIB                        12                          72
  STAGE IIIC                        16                          39
  STAGE IV                          18                          45
  STAGE IVA                          6                          18
  STAGE IVB                          1                           1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK  3(5P12) MUTATED     2  23  78  13
  AMP PEAK  3(5P12) WILD-TYPE  18  82 339  56
D3V5, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  T1                         2                          18
  T2                        23                          82
  T3                        78                         339
  T4                        13                          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
  AMP PEAK  3(5P12) MUTATED    54  32  29
  AMP PEAK  3(5P12) WILD-TYPE 292 118  86
D3V6, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  N0                        54                         292
  N1                        32                         118
  N2                        29                          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"
D3V7, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    77  24
  AMP PEAK  3(5P12) WILD-TYPE 376  64
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     77   24
  AMP PEAK  3(5P12) WILD-TYPE  376   64
   clus
vv  AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  0                        77                         376
  1                        24                          64
[1] 2 2
[1] FALSE
D3V8, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    52  64
  AMP PEAK  3(5P12) WILD-TYPE 237 261
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     52   64
  AMP PEAK  3(5P12) WILD-TYPE  237  261
        clus
vv       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  FEMALE                        52                         237
  MALE                          64                         261
[1] 2 2
[1] FALSE
D3V9, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED    89   9
  AMP PEAK  3(5P12) WILD-TYPE 393  20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED     89    9
  AMP PEAK  3(5P12) WILD-TYPE  393   20
     clus
vv    AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  NO                         89                         393
  YES                         9                          20
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                     67
  AMP PEAK  3(5P12) WILD-TYPE                  315
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                               9
  AMP PEAK  3(5P12) WILD-TYPE                            53
                             vv
clus                          RECTAL ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                      40
  AMP PEAK  3(5P12) WILD-TYPE                   106
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  3(5P12) MUTATED                                0
  AMP PEAK  3(5P12) WILD-TYPE                             13
D3V10, multiclass
                                clus
vv                               AMP PEAK  3(5P12) MUTATED
  COLON ADENOCARCINOMA                                  67
  COLON MUCINOUS ADENOCARCINOMA                          9
  RECTAL ADENOCARCINOMA                                 40
  RECTAL MUCINOUS ADENOCARCINOMA                         0
                                clus
vv                               AMP PEAK  3(5P12) WILD-TYPE
  COLON ADENOCARCINOMA                                   315
  COLON MUCINOUS ADENOCARCINOMA                           53
  RECTAL ADENOCARCINOMA                                  106
  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"
                             vv
clus                           R0  R1  R2  RX
  AMP PEAK  3(5P12) MUTATED    84   1  13   3
  AMP PEAK  3(5P12) WILD-TYPE 362   5  24  26
D3V11, multiclass
    clus
vv   AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  R0                        84                         362
  R1                         1                           5
  R2                        13                          24
  RX                         3                          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"
D3V12, continuous
D3V13, binary
                             cls
clus                            0   1
  AMP PEAK  3(5P12) MUTATED     1  62
  AMP PEAK  3(5P12) WILD-TYPE   4 290
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  3(5P12) MUTATED      1   62
  AMP PEAK  3(5P12) WILD-TYPE    4  290
                        clus
vv                       AMP PEAK  3(5P12) MUTATED AMP PEAK  3(5P12) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        62                         290
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(6P21.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(6P21.1) MUTATED   116  30
  AMP PEAK  4(6P21.1) WILD-TYPE 350  98
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                          146                           448 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           30                            98 
$`AMP PEAK  4(6P21.1) MUTATED`
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3867 TCGA-G4-6294 TCGA-G4-6310 
       13.02        19.99        85.05        24.03        28.21        63.62 
TCGA-G4-6625 TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 
       91.79        10.39        19.99        36.03        31.00        21.24 
TCGA-G5-6233 TCGA-G5-6641 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-3810 TCGA-A6-4107 
       18.28        26.43        43.43        44.91        36.53        32.45 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 
       30.44        29.19        22.52        25.08        25.18        20.61 
TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3553 
       23.87        56.25        29.00        29.00        12.99        24.00 
TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 
       13.94         2.01        15.02        37.05        10.06        35.05 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3968 
       17.03        10.06        27.02         2.01        20.98        21.99 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A01I 
       27.02         7.96        13.94        34.03        27.02        31.00 
TCGA-AA-A02E TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 
        2.96        40.96        22.42        26.47        14.50         0.95 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-CA-6719 
        0.20        17.26         5.65        22.36        65.00        14.30 
TCGA-CK-4952 TCGA-CK-5914 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 
       15.62        21.99         8.02        13.02        29.06        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6169 TCGA-CM-6170 
       30.08        32.02         5.03        15.02        13.02        15.02 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6538 
       19.59        56.09        55.92        25.48        15.12        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       12.49         7.53        10.13         9.04        13.41        11.38 
TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       13.32         7.50        14.04       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6854 TCGA-G4-6295 
        8.61        31.96        35.74         1.55         0.53         8.35 
TCGA-G4-6297 TCGA-G4-6311 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YW 
       82.39        39.42        46.75        10.98        12.79        29.46 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       21.90        38.70        46.92        43.04        37.97        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 
       29.98        24.36        65.98        36.03        24.00        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 
       34.03        34.03         6.05        19.99        20.98        29.98 
TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
        1.02         1.02        14.04         1.02         3.98        46.03 
TCGA-AG-A016 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-DC-4745 
        9.07        27.55         6.05        13.78        47.44        21.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE 
       31.00        12.00        31.00        51.98        25.05       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        49.51 
TCGA-F5-6702 TCGA-F5-6810 
       28.57         0.39 

$`AMP PEAK  4(6P21.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       19.07        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
        6.05         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 
      106.75       100.01         1.94        49.08         5.88        23.51 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 
       35.93        22.09        35.80        26.17        79.69        17.85 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
        8.02        13.94        17.03        17.03        25.97        15.95 
TCGA-AG-A023 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       51.98        55.76        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
        9.53        39.45        43.76        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       42.28        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 
       34.65        32.75        32.91        31.63        33.53        23.61 
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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
        8.38        21.76        24.69        24.39        20.12        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 
       20.28        16.24        24.92        61.84         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 
        0.00        26.01        14.01        33.99        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       20.98        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       50.04        47.05        47.01        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99         0.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 
       38.99        36.95        37.02         0.00         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
        0.00        36.03        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       17.03        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        16.08        13.05        34.06        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K 
       27.02        38.04        19.00        30.02        18.05        18.05 
TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K 
       15.02        15.02        10.98        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         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02        51.98        39.98         2.01         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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       83.24        24.53         5.79        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31        33.01        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94         5.13        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.36        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        17.56       148.01        85.45        70.16 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5344 
       20.02        37.02        25.02        26.04        27.02        22.03 
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-6171 
       29.03        16.04        21.99        14.99        12.99        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-D5-6529 TCGA-D5-6530 
       10.06        12.03        45.40        54.61        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 
       17.75        18.25        43.27        17.85         4.80        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 
       13.35        12.00        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-A1DB 
      130.65        92.75        49.91        12.59       140.38        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-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 
      119.93        35.97        60.79        11.11        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       47.41        35.31       133.18        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 
       53.62        44.68        55.04        85.48        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       26.43        26.04        13.78        74.79        18.18        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       19.33         9.93        15.65        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 
        8.42        31.30        60.13        11.90        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       17.23        13.55        34.49        16.83        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       20.05         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
        0.99        15.95         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04        19.99        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       19.99        28.04        36.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         1.02         1.02        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        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       43.20        26.43        19.46        33.17        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 
       78.12         7.17        25.05        26.04        13.97        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       57.24        32.61         3.48         4.18        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        16.34        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-F5-6571 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        42.35        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                          0.2                           0.0 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                       129.27                        148.01 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                        22.75                         21.60 
[1] "0.2 - 129.3 (22.8)" "0.0 - 148.0 (21.6)"
[1] "hr=" "1"  
D4V2, continuous
D4V3, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED   100  51
  AMP PEAK  4(6P21.1) WILD-TYPE 348 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED    100   51
  AMP PEAK  4(6P21.1) WILD-TYPE  348  111
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  COLON                          100                           348
  RECTUM                          51                           111
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  4(6P21.1) MUTATED        21        0        5        32         1
  AMP PEAK  4(6P21.1) WILD-TYPE      83        1       32       140        11
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  4(6P21.1) MUTATED           0         4          5         26
  AMP PEAK  4(6P21.1) WILD-TYPE         2        20         10         58
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  4(6P21.1) MUTATED           22       19        12         1
  AMP PEAK  4(6P21.1) WILD-TYPE         33       44        12         1
D4V4, multiclass
            clus
vv           AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  STAGE I                             21                            83
  STAGE IA                             0                             1
  STAGE II                             5                            32
  STAGE IIA                           32                           140
  STAGE IIB                            1                            11
  STAGE IIC                            0                             2
  STAGE III                            4                            20
  STAGE IIIA                           5                            10
  STAGE IIIB                          26                            58
  STAGE IIIC                          22                            33
  STAGE IV                            19                            44
  STAGE IVA                           12                            12
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  4(6P21.1) MUTATED     6  20 112  15
  AMP PEAK  4(6P21.1) WILD-TYPE  14  85 305  54
D4V5, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  T1                           6                            14
  T2                          20                            85
  T3                         112                           305
  T4                          15                            54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  4(6P21.1) MUTATED    66  41  45
  AMP PEAK  4(6P21.1) WILD-TYPE 280 109  70
D4V6, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  N0                          66                           280
  N1                          41                           109
  N2                          45                            70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED   102  31
  AMP PEAK  4(6P21.1) WILD-TYPE 351  57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED    102   31
  AMP PEAK  4(6P21.1) WILD-TYPE  351   57
   clus
vv  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  0                         102                           351
  1                          31                            57
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED    65  89
  AMP PEAK  4(6P21.1) WILD-TYPE 224 236
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     65   89
  AMP PEAK  4(6P21.1) WILD-TYPE  224  236
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  FEMALE                          65                           224
  MALE                            89                           236
[1] 2 2
[1] FALSE
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED   114  10
  AMP PEAK  4(6P21.1) WILD-TYPE 368  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED    114   10
  AMP PEAK  4(6P21.1) WILD-TYPE  368   19
     clus
vv    AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  NO                          114                           368
  YES                          10                            19
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  4(6P21.1) MUTATED                     90
  AMP PEAK  4(6P21.1) WILD-TYPE                  292
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(6P21.1) MUTATED                               9
  AMP PEAK  4(6P21.1) WILD-TYPE                            53
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  4(6P21.1) MUTATED                      50
  AMP PEAK  4(6P21.1) WILD-TYPE                    96
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  4(6P21.1) MUTATED                                1
  AMP PEAK  4(6P21.1) WILD-TYPE                             12
D4V10, multiclass
                                clus
vv                               AMP PEAK  4(6P21.1) MUTATED
  COLON ADENOCARCINOMA                                    90
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   50
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK  4(6P21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     292
  COLON MUCINOUS ADENOCARCINOMA                             53
  RECTAL ADENOCARCINOMA                                     96
  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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  4(6P21.1) MUTATED   107   1  14   5
  AMP PEAK  4(6P21.1) WILD-TYPE 339   5  23  24
D4V11, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  R0                         107                           339
  R1                           1                             5
  R2                          14                            23
  RX                           5                            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"
D4V12, continuous
D4V13, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED     0  94
  AMP PEAK  4(6P21.1) WILD-TYPE   5 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED      0   94
  AMP PEAK  4(6P21.1) WILD-TYPE    5  258
                        clus
vv                       AMP PEAK  4(6P21.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          94
                        clus
vv                       AMP PEAK  4(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           258
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(7P21.3) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(7P21.3) MUTATED   273  76
  AMP PEAK  5(7P21.3) WILD-TYPE 193  52
  AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE 
                          349                           245 
  AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE 
                           76                            52 
$`AMP PEAK  5(7P21.3) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3524 
       45.60        13.94        24.16         1.02        58.03        36.03 
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       13.02        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3976 
       85.05        14.93        24.03        29.98        24.00        26.01 
TCGA-AA-A00L TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6608 
       38.04        21.37        15.52        75.95       106.75         1.94 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 
        5.88        28.21        23.51        63.62        35.93        91.79 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       17.85        10.39        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 
       25.97        15.95        36.03        31.00        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       55.76        26.43        15.62         4.80        12.66         1.61 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 
       39.45        43.76        43.76        43.43        44.91        35.11 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        34.65        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 
       31.63        30.44        29.19        29.16        22.52        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-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       16.24        24.92        56.25         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        1.02        37.05        35.01         6.97        38.99         9.07 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3553 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       24.00        61.02        78.08        54.02         2.01        14.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       15.02        11.01         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3852 
       35.05         0.99        36.95        37.02        10.06         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       32.05         0.99        31.07        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       31.00        24.00        20.98        21.99        16.08        34.06 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       27.02        27.02        13.94        19.00        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       17.03        15.02        32.02        33.04        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y 
       51.98         2.96         2.01         5.03         0.92        39.98 
TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       16.44         0.46        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4682 
        0.20        17.82        17.26        18.84       109.28        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        88.21        49.41        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
        5.23         3.19        12.36        12.46        12.39        12.59 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CM-4744 
       14.30        17.56       148.01        85.45        21.99        20.02 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       25.02         8.02        27.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       22.98        32.02         5.03        15.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        14.04        29.03        16.04        14.99        12.99 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        11.01        11.08        11.08        11.01        10.06 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       19.59        55.92        17.75        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.80        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0XD 
       12.43        14.30         9.04        13.41        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       38.20        92.75        49.91        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H 
       44.32       131.51         7.76        14.04        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6808 
       95.18         8.61        31.96        35.74         1.55        33.67 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 
        0.53        47.41       133.18        82.39        74.56        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        55.04        39.42        61.91        36.00        26.43 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GA TCGA-NH-A6GB 
       13.78        46.75        74.79        18.18         9.93        15.65 
TCGA-NH-A6GC TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 
       12.79         8.42        21.90        38.70        70.03        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       39.48        17.23        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 
       24.36        20.02        86.63        65.98         7.07        36.03 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3599 TCGA-AG-3600 
       24.00        46.03        34.03        34.03        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 
        0.99        15.95        19.99        20.98        29.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        0.99        19.99        17.95        35.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A016 
       19.99        36.03         1.02        46.03         6.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 
        1.02         1.02         1.94        38.96        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       43.20        27.55        26.43         6.05        33.17        13.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 
      129.27        24.13         3.48         4.18        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.34        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       13.64        11.97         8.45         9.96        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
        0.39        32.19        36.49        19.66        11.87        12.46 
TCGA-G5-6572 
       47.08 

$`AMP PEAK  5(7P21.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       24.33        14.53        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3672 
       19.07        34.03         0.99        17.95        23.01         0.92 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       19.04        19.04        31.07        12.99         2.01        50.99 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 
       24.00        19.07        21.99        39.06        25.08        10.88 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
      100.01        49.08        22.09        35.80        26.17        79.69 
TCGA-AG-3580 TCGA-AG-A023 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 
        8.02        51.98         9.53        46.65        42.90        42.28 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       16.57        37.05        32.75        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 
       22.06        32.71        27.09         8.38        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A567 TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3514 
       20.12        19.66        61.84         3.02        63.98         1.02 
TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 
        1.02        19.07        29.00        21.01        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3710 
       13.94         6.97        50.04        47.05        47.01        26.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        38.99         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3930 
       17.03         0.00        33.07        36.03        53.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 
       33.01        26.01        34.03         2.01        13.05        25.02 
TCGA-AA-3989 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
        7.96        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D 
       27.02         0.99        14.99        34.98        15.02        10.98 
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-A02F TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F 
        1.02         1.02        39.98        22.03        41.00        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-A69D 
       12.16        83.24         0.92        27.09        21.44        17.85 
TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       19.33        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
        6.77        11.74        12.69        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       10.06        70.16        15.62        51.32        21.14        82.95 
TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5349 
        2.01       124.27        23.05        37.02        26.04        30.08 
TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 
       15.02        12.00        21.99        13.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 
       13.05        12.03        45.40        54.61        56.09        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 
       20.42        18.25        16.14        15.58        12.39         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1D0 
       11.64        13.35        12.00        11.38       119.70       130.65 
TCGA-DM-A1D7 TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
       13.32       135.65       139.17        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 
       60.79        98.24        11.11        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6295 
       34.42        41.42        43.04        13.25        35.31         8.35 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6322 TCGA-NH-A50U TCGA-NH-A50V 
       67.30        53.62        85.48        26.04        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       19.33        16.80        42.77        29.46        32.98        31.30 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-6672 
       60.13        11.90        43.04        13.55        37.97        24.59 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3586 
       11.84        36.03        12.00        32.02        20.05         1.02 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       34.03         2.01        50.04         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       32.98        19.04         1.02        36.95        13.02        14.01 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 
       25.02        32.02        28.04        14.04         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       13.94        23.01        37.02        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6622 TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 
        2.50        19.46        44.78        26.04        44.02        25.97 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 
       51.48        32.61        20.55        19.96        17.00        16.41 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46        49.51        37.18        38.14 

  AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE 
                            0                             0 
  AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE 
                       148.01                        139.17 
  AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE 
                        21.99                         22.03 
[1] "0.0 - 148.0 (22.0)" "0.0 - 139.2 (22.0)"
[1] "hr=" "1"  
D5V2, continuous
D5V3, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.3) MUTATED   251 108
  AMP PEAK  5(7P21.3) WILD-TYPE 197  54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.3) MUTATED    251  108
  AMP PEAK  5(7P21.3) WILD-TYPE  197   54
        clus
vv       AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE
  COLON                          251                           197
  RECTUM                         108                            54
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  5(7P21.3) MUTATED        57        1       20        76         3
  AMP PEAK  5(7P21.3) WILD-TYPE      47        0       17        96         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  5(7P21.3) MUTATED           1        14         11         63
  AMP PEAK  5(7P21.3) WILD-TYPE         1        10          4         21
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  5(7P21.3) MUTATED           38       43        18         1
  AMP PEAK  5(7P21.3) WILD-TYPE         17       20         6         1
D5V4, multiclass
            clus
vv           AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE
  STAGE I                             57                            47
  STAGE IA                             1                             0
  STAGE II                            20                            17
  STAGE IIA                           76                            96
  STAGE IIB                            3                             9
  STAGE IIC                            1                             1
  STAGE III                           14                            10
  STAGE IIIA                          11                             4
  STAGE IIIB                          63                            21
  STAGE IIIC                          38                            17
  STAGE IV                            43                            20
  STAGE IVA                           18                             6
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  5(7P21.3) MUTATED    13  60 246  39
  AMP PEAK  5(7P21.3) WILD-TYPE   7  45 171  30
D5V5, multiclass
    clus
vv   AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE
  T1                          13                             7
  T2                          60                            45
  T3                         246                           171
  T4                          39                            30
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  AMP PEAK  5(7P21.3) MUTATED   172 109  77
  AMP PEAK  5(7P21.3) WILD-TYPE 174  41  38
D5V6, multiclass
    clus
vv   AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE
  N0                         172                           174
  N1                         109                            41
  N2                          77                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.3) MUTATED   251  62
  AMP PEAK  5(7P21.3) WILD-TYPE 202  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.3) MUTATED    251   62
  AMP PEAK  5(7P21.3) WILD-TYPE  202   26
   clus
vv  AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE
  0                         251                           202
  1                          62                            26
[1] 2 2
[1] FALSE
D5V8, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.3) MUTATED   168 193
  AMP PEAK  5(7P21.3) WILD-TYPE 121 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.3) MUTATED    168  193
  AMP PEAK  5(7P21.3) WILD-TYPE  121  132
        clus
vv       AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE
  FEMALE                         168                           121
  MALE                           193                           132
[1] 2 2
[1] FALSE
D5V9, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.3) MUTATED   278  20
  AMP PEAK  5(7P21.3) WILD-TYPE 204   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.3) MUTATED    278   20
  AMP PEAK  5(7P21.3) WILD-TYPE  204    9
     clus
vv    AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE
  NO                          278                           204
  YES                          20                             9
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  AMP PEAK  5(7P21.3) MUTATED                    225
  AMP PEAK  5(7P21.3) WILD-TYPE                  157
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(7P21.3) MUTATED                              25
  AMP PEAK  5(7P21.3) WILD-TYPE                            37
                               vv
clus                            RECTAL ADENOCARCINOMA
  AMP PEAK  5(7P21.3) MUTATED                     102
  AMP PEAK  5(7P21.3) WILD-TYPE                    44
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  5(7P21.3) MUTATED                                5
  AMP PEAK  5(7P21.3) WILD-TYPE                              8
D5V10, multiclass
                                clus
vv                               AMP PEAK  5(7P21.3) MUTATED
  COLON ADENOCARCINOMA                                   225
  COLON MUCINOUS ADENOCARCINOMA                           25
  RECTAL ADENOCARCINOMA                                  102
  RECTAL MUCINOUS ADENOCARCINOMA                           5
                                clus
vv                               AMP PEAK  5(7P21.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     157
  COLON MUCINOUS ADENOCARCINOMA                             37
  RECTAL ADENOCARCINOMA                                     44
  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"
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  5(7P21.3) MUTATED   259   5  25  14
  AMP PEAK  5(7P21.3) WILD-TYPE 187   1  12  15
D5V11, multiclass
    clus
vv   AMP PEAK  5(7P21.3) MUTATED AMP PEAK  5(7P21.3) WILD-TYPE
  R0                         259                           187
  R1                           5                             1
  R2                          25                            12
  RX                          14                            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"
D5V12, continuous
D5V13, binary
                               cls
clus                              0   1
  AMP PEAK  5(7P21.3) MUTATED     3 217
  AMP PEAK  5(7P21.3) WILD-TYPE   2 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(7P21.3) MUTATED      3  217
  AMP PEAK  5(7P21.3) WILD-TYPE    2  135
                        clus
vv                       AMP PEAK  5(7P21.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         217
                        clus
vv                       AMP PEAK  5(7P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           135
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(8P11.23) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  6(8P11.23) MUTATED   157  44
  AMP PEAK  6(8P11.23) WILD-TYPE 309  84
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                           201                            393 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                            44                             84 
$`AMP PEAK  6(8P11.23) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3524 
       24.33        45.60        13.94        24.16         1.02        36.03 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 
       19.99         6.05        19.00        19.04        19.04        31.07 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AZ-4681 TCGA-AZ-6608 
       24.03        12.99        24.00        21.99       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       49.08         5.88        63.62        15.95        31.00        51.98 
TCGA-G5-6233 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2675 TCGA-A6-3807 
       18.28        15.62        12.66        39.45        43.43        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-A6-6782 TCGA-A6-A5ZU TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 
       20.28         9.63        37.05        35.01         6.97         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 
       19.07         0.00        29.00        26.01        12.99        33.99 
TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       20.98        78.08         6.97        54.02        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3841 
       47.01         5.98        37.05         5.03        10.06        36.95 
TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3975 
       17.03         0.00        31.07        18.05        24.00        34.06 
TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A01D TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 
       18.05         0.99        10.98         1.02        37.02        51.98 
TCGA-AA-A02O TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-6004 
        0.92        12.16         5.79        27.42        16.44        27.09 
TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       16.31        21.44        17.26         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 
       22.36        62.79        88.21        49.41         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CK-4948 TCGA-CK-4952 
       12.36        12.46        12.59        12.59       148.01        15.62 
TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       51.32         2.01        20.02        37.02        25.02         8.02 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       15.02        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5541 TCGA-D5-6529 
       11.01        11.08        11.08        10.06        55.92        20.19 
TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6923 
       25.48         4.80        17.13        16.14         7.53        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       14.30         9.04        11.38        10.26       119.70        38.20 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6569 TCGA-F4-6570 
        7.50        44.32       117.07        98.24        35.74         6.18 
TCGA-F4-6807 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6311 TCGA-G4-6320 
       43.04        67.30        65.85        53.62        39.42        26.43 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5YX 
       46.75        74.79        18.18        15.65        29.46        32.98 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 
        8.42        38.70        70.03        37.74        20.02        24.59 
TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3592 
       65.98        36.03        36.03        24.00        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        2.01         0.99        36.95        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A032 TCGA-AH-6544 
       32.02        36.03         1.02        46.03        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       43.20        27.55         6.05        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A1DC 
        7.17        31.00        51.98        10.98        25.05        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         3.48        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        49.51        28.57        32.19 
TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6572 
       19.66        12.46        47.08 

$`AMP PEAK  6(8P11.23) WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       14.53        58.03        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3870 
       19.99         0.92        36.00        85.05        14.93        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       24.00         2.01        50.99        26.01        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
      100.01        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 
       13.94        19.99        17.03        17.03        25.97        36.03 
TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 
       21.24        55.76        26.43         4.80         1.61         9.53 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       43.76        46.65        43.76        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       35.11        16.57        37.05        37.25        37.02        32.75 
TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        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        56.25         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-3518 
        7.04         3.02         1.02        63.98        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
        9.07        29.00        14.01        21.01        24.00        29.95 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
       13.94        61.02         2.01        47.05        15.02        11.01 
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-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3866 
       33.07        36.03        32.05         0.99        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       27.02        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3977 
       34.03         2.01        21.99        16.08        13.05        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        34.03        18.05         4.01        27.02        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       33.04         1.02        26.01         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       83.24        24.53        22.42        26.47         0.46         0.92 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D 
       14.50         0.95        33.01         0.20        17.82        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4684 
       19.33        18.84       109.28        58.39         1.41        65.00 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 
        6.77        12.10        29.56         5.23        11.74        12.39 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.20        12.76        10.06        14.30        17.56        85.45 
TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       70.16        21.99        21.14        82.95       124.27        23.05 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       26.04        27.02        13.02        29.06        22.03        30.08 
TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 
       17.03        12.00        14.04        16.04        15.02        14.04 
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        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 
       19.59        56.09        20.42        17.75        18.25        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       15.12        17.85        12.49        15.58        12.39        10.13 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A0XD 
        9.44        11.64        13.41        13.35        12.00        24.43 
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-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-A28M TCGA-F4-6459 
       81.37       119.93        35.97        60.79        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       31.96        11.11        35.74        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6306 TCGA-G4-6307 
      133.18         8.35        82.39        74.56        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50U 
       85.48        61.91        36.00        26.04        13.78        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        12.79        16.80        42.77 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 
       31.30        21.90        60.13        11.90        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 
       17.23        43.04        13.55        37.97        34.49        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       16.83        24.36        86.63        11.84        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
        7.07        20.05         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
       12.03         6.05        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3894 
       19.04        19.99         1.02        17.95        13.02        14.01 
TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 
       25.02        19.99        28.04        14.04         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
        2.50        26.43        19.46        33.17        13.78        44.78 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       44.02        25.97        25.05        12.62       126.44       129.27 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         4.18        20.55        19.96        20.91        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       17.69        16.34        16.41         8.61        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       11.97         8.45         9.96        42.35         0.39        36.49 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       37.18        38.14        11.87 

  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                             0                              0 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE 
                          24.0                           21.9 
[1] "0.0 - 148.0 (24.0)" "0.0 - 140.4 (21.9)"
[1] "hr=" "1"  
D6V2, continuous
D6V3, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED   157  53
  AMP PEAK  6(8P11.23) WILD-TYPE 291 109
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED    157   53
  AMP PEAK  6(8P11.23) WILD-TYPE  291  109
        clus
vv       AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  COLON                           157                            291
  RECTUM                           53                            109
[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        53         4
  AMP PEAK  6(8P11.23) WILD-TYPE      67        1       20       119         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  6(8P11.23) MUTATED           2         8          4         24
  AMP PEAK  6(8P11.23) WILD-TYPE         0        16         11         60
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  6(8P11.23) MUTATED           24       22         9         0
  AMP PEAK  6(8P11.23) WILD-TYPE         31       41        15         2
D6V4, multiclass
            clus
vv           AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  STAGE I                              37                             67
  STAGE IA                              0                              1
  STAGE II                             17                             20
  STAGE IIA                            53                            119
  STAGE IIB                             4                              8
  STAGE IIC                             2                              0
  STAGE III                             8                             16
  STAGE IIIA                            4                             11
  STAGE IIIB                           24                             60
  STAGE IIIC                           24                             31
  STAGE IV                             22                             41
  STAGE IVA                             9                             15
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  6(8P11.23) MUTATED     4  38 143  24
  AMP PEAK  6(8P11.23) WILD-TYPE  16  67 274  45
D6V5, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  T1                            4                             16
  T2                           38                             67
  T3                          143                            274
  T4                           24                             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  6(8P11.23) MUTATED   119  46  43
  AMP PEAK  6(8P11.23) WILD-TYPE 227 104  72
D6V6, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  N0                          119                            227
  N1                           46                            104
  N2                           43                             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"
D6V7, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED   148  31
  AMP PEAK  6(8P11.23) WILD-TYPE 305  57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED    148   31
  AMP PEAK  6(8P11.23) WILD-TYPE  305   57
   clus
vv  AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  0                          148                            305
  1                           31                             57
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED    95 115
  AMP PEAK  6(8P11.23) WILD-TYPE 194 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED     95  115
  AMP PEAK  6(8P11.23) WILD-TYPE  194  210
        clus
vv       AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  FEMALE                           95                            194
  MALE                            115                            210
[1] 2 2
[1] FALSE
D6V9, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED   163  11
  AMP PEAK  6(8P11.23) WILD-TYPE 319  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED    163   11
  AMP PEAK  6(8P11.23) WILD-TYPE  319   18
     clus
vv    AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  NO                           163                            319
  YES                           11                             18
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  6(8P11.23) MUTATED                    140
  AMP PEAK  6(8P11.23) WILD-TYPE                  242
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(8P11.23) MUTATED                              16
  AMP PEAK  6(8P11.23) WILD-TYPE                            46
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK  6(8P11.23) MUTATED                      51
  AMP PEAK  6(8P11.23) WILD-TYPE                    95
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  6(8P11.23) MUTATED                                2
  AMP PEAK  6(8P11.23) WILD-TYPE                             11
D6V10, multiclass
                                clus
vv                               AMP PEAK  6(8P11.23) MUTATED
  COLON ADENOCARCINOMA                                    140
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                    51
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK  6(8P11.23) WILD-TYPE
  COLON ADENOCARCINOMA                                      242
  COLON MUCINOUS ADENOCARCINOMA                              46
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  6(8P11.23) MUTATED   144   1  16  15
  AMP PEAK  6(8P11.23) WILD-TYPE 302   5  21  14
D6V11, multiclass
    clus
vv   AMP PEAK  6(8P11.23) MUTATED AMP PEAK  6(8P11.23) WILD-TYPE
  R0                          144                            302
  R1                            1                              5
  R2                           16                             21
  RX                           15                             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
D6V13, binary
                                cls
clus                               0   1
  AMP PEAK  6(8P11.23) MUTATED     1 128
  AMP PEAK  6(8P11.23) WILD-TYPE   4 224
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.23) MUTATED      1  128
  AMP PEAK  6(8P11.23) WILD-TYPE    4  224
                        clus
vv                       AMP PEAK  6(8P11.23) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          128
                        clus
vv                       AMP PEAK  6(8P11.23) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            224
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(8P11.21) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(8P11.21) MUTATED   192  51
  AMP PEAK  7(8P11.21) WILD-TYPE 274  77
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                           243                            351 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                            51                             77 
$`AMP PEAK  7(8P11.21) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3524 
       24.33        45.60        13.94        24.16         1.02        36.03 
TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 
       13.02        19.99        19.99        19.00        36.00        19.04 
TCGA-AA-3715 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AZ-4681 
       19.04        24.03        12.99        24.00        21.99       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-AG-A014 TCGA-AG-A01N 
        1.94        49.08         5.88        63.62        15.95        31.00 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4T-AA8H 
       51.98        18.28        55.76        26.43        15.62        12.66 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-3807 
       39.45        43.76        43.76        43.43        35.11        34.65 
TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       32.45        31.63        23.61        32.71        29.16        27.09 
TCGA-A6-6648 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3495 
       25.18        20.28        61.84         9.63         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 
       35.01         6.97         1.02        19.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3558 
       26.01        12.99        14.01        33.99        24.00        20.98 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3841 
       15.02         5.98        37.05         5.03        10.06        36.95 
TCGA-AA-3846 TCGA-AA-3852 TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 
       17.03         0.00        31.07        27.02        18.05         2.01 
TCGA-AA-3941 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R 
       24.00        16.08        34.06        19.00        18.05         0.99 
TCGA-AA-A00U TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02W 
       17.03         1.02        37.02        51.98         0.92        41.00 
TCGA-AD-5900 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-6004 
       12.16         5.79        27.42        16.44         0.92        27.09 
TCGA-AY-6197 TCGA-AY-A54L TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5403 
       21.44        17.26        32.94         5.13        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       88.21        49.41         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 
       12.36        12.46        12.59        14.30       148.01        15.62 
TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 
       51.32         2.01        20.02        37.02        25.02         8.02 
TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 
       27.02        22.98        30.08        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        15.02        29.03        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5541 
       13.02        11.01        11.08        11.08        10.06        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 
       20.19        25.48         4.80        17.13        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1DA 
       11.38        10.26       119.70        38.20       130.65         7.50 
TCGA-DM-A1DB TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 
       44.32       117.07        98.24         8.61        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 
        6.18        34.42        43.04         8.35        74.56        67.30 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 
       53.62        44.68        39.42        26.43        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       18.18        10.98        15.65        29.46        32.98         8.42 
TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 
       38.70        70.03        20.02        24.59        65.98        36.03 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 
       36.03        24.00         1.02        34.03        34.03         2.01 
TCGA-AG-3605 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
        0.99        32.98        19.04         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        46.03 
TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       23.01         9.07         1.02         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 
       38.56         2.50        43.20        27.55         6.05        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       48.20        78.12         7.17        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       10.98        25.05        25.05       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6514 
      129.27        24.13         3.48        17.00        15.85        16.31 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 
       11.51        10.78        13.64        49.51        28.57        32.19 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

$`AMP PEAK  7(8P11.21) WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 
       14.53        58.03        13.02        24.03        37.05         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3662 
       19.07        34.03         0.99        17.95        23.01         6.05 
TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 
        0.92        85.05        14.93        31.07        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
        2.01        50.99        26.01        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 
       21.37        15.52        25.08        10.88        75.95       100.01 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        23.51        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 
       91.79        79.69        17.85        10.39         8.02        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 TCGA-BM-6198 
       19.99        17.03        17.03        25.97        36.03        21.24 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 
        4.80         1.61         9.53        46.65        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       44.91        16.57        37.05        37.25        37.02        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5664 
       36.53        32.91        30.44        29.19        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 
       22.06        22.52        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-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       16.24        24.92        56.25         5.03         7.04         3.02 
TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3549 
       63.98        38.99         1.02         9.07         0.00        21.01 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3680 
       29.95        13.94        61.02         2.01        47.05        11.01 
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-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       15.95        38.99        37.02         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3866 
       33.07        36.03        32.05         0.99        53.00        17.03 
TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       31.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       21.99        13.05        25.02        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N 
       13.94        38.04        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C 
       27.02        42.02        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02E 
        1.02        35.01        33.04         1.02        26.01         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         5.03        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 
       40.96        83.24        24.53        22.42        26.47         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6386 
       14.50        16.31         0.95        33.01         0.20        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5796 
        5.65        65.00         6.77        12.10        29.56        12.39 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.20        12.76        10.06        17.56        85.45 
TCGA-CK-4951 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       70.16        21.99        21.14        82.95       124.27        23.05 
TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5868 TCGA-CM-6162 
       26.04        13.02        29.06        22.03        17.03        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6674 
       14.04        16.04        21.99        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 
       13.05        11.01        12.03        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       56.09        20.42        17.75        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       17.85        12.49        12.39         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-DM-A0XD TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       12.00        24.43        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
      140.38       131.51       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-A28M 
       26.47        81.37       119.93        35.97        60.79        95.18 
TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 
       31.96        11.11        47.87         1.55        41.42        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
       13.25         0.53        47.41        35.31       133.18        82.39 
TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 
       65.85        55.04        85.48        61.91        36.00        26.04 
TCGA-G4-6323 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 
       13.78        19.33        19.33         9.93        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 
       42.77        31.30        21.90        60.13        11.90        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N 
       37.74        29.98        16.83        24.36        86.63        11.84 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 
       12.00        32.02         7.07        20.05        46.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       50.04        12.03         6.05        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98        37.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 
       19.99        17.95        13.02        35.01        14.01        25.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       19.99        36.03         3.98        20.98        13.94         6.02 
TCGA-AG-A011 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6897 
       37.02         1.02        49.97        61.97        41.00        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-DC-4745 TCGA-DC-4749 
       19.46        33.17        13.78        44.78        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       26.04        31.00        12.00        44.02        25.97        12.62 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         4.18        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 
       18.28        17.69        16.34        16.41         8.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       11.97         8.45         9.96        42.35         0.39        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       19.66        37.18        38.14 

  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                             0                              0 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE 
                         22.98                          21.99 
[1] "0.0 - 148.0 (23.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED   184  70
  AMP PEAK  7(8P11.21) WILD-TYPE 264  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED    184   70
  AMP PEAK  7(8P11.21) WILD-TYPE  264   92
        clus
vv       AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  COLON                           184                            264
  RECTUM                           70                             92
[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        65         4
  AMP PEAK  7(8P11.21) WILD-TYPE      63        1       16       107         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  7(8P11.21) MUTATED           2        10          7         30
  AMP PEAK  7(8P11.21) WILD-TYPE         0        14          8         54
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  7(8P11.21) MUTATED           23       34         9         0
  AMP PEAK  7(8P11.21) WILD-TYPE         32       29        15         2
D7V4, multiclass
            clus
vv           AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  STAGE I                              41                             63
  STAGE IA                              0                              1
  STAGE II                             21                             16
  STAGE IIA                            65                            107
  STAGE IIB                             4                              8
  STAGE IIC                             2                              0
  STAGE III                            10                             14
  STAGE IIIA                            7                              8
  STAGE IIIB                           30                             54
  STAGE IIIC                           23                             32
  STAGE IV                             34                             29
  STAGE IVA                             9                             15
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  7(8P11.21) MUTATED     5  45 176  27
  AMP PEAK  7(8P11.21) WILD-TYPE  15  60 241  42
D7V5, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  T1                            5                             15
  T2                           45                             60
  T3                          176                            241
  T4                           27                             42
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  7(8P11.21) MUTATED   143  56  53
  AMP PEAK  7(8P11.21) WILD-TYPE 203  94  62
D7V6, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  N0                          143                            203
  N1                           56                             94
  N2                           53                             62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED   178  43
  AMP PEAK  7(8P11.21) WILD-TYPE 275  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED    178   43
  AMP PEAK  7(8P11.21) WILD-TYPE  275   45
   clus
vv  AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  0                          178                            275
  1                           43                             45
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED   111 143
  AMP PEAK  7(8P11.21) WILD-TYPE 178 182
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED    111  143
  AMP PEAK  7(8P11.21) WILD-TYPE  178  182
        clus
vv       AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  FEMALE                          111                            178
  MALE                            143                            182
[1] 2 2
[1] FALSE
D7V9, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED   198  11
  AMP PEAK  7(8P11.21) WILD-TYPE 284  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED    198   11
  AMP PEAK  7(8P11.21) WILD-TYPE  284   18
     clus
vv    AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  NO                           198                            284
  YES                           11                             18
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  7(8P11.21) MUTATED                    164
  AMP PEAK  7(8P11.21) WILD-TYPE                  218
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(8P11.21) MUTATED                              19
  AMP PEAK  7(8P11.21) WILD-TYPE                            43
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK  7(8P11.21) MUTATED                      65
  AMP PEAK  7(8P11.21) WILD-TYPE                    81
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  7(8P11.21) MUTATED                                3
  AMP PEAK  7(8P11.21) WILD-TYPE                             10
D7V10, multiclass
                                clus
vv                               AMP PEAK  7(8P11.21) MUTATED
  COLON ADENOCARCINOMA                                    164
  COLON MUCINOUS ADENOCARCINOMA                            19
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK  7(8P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      218
  COLON MUCINOUS ADENOCARCINOMA                              43
  RECTAL ADENOCARCINOMA                                      81
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  7(8P11.21) MUTATED   173   2  22  16
  AMP PEAK  7(8P11.21) WILD-TYPE 273   4  15  13
D7V11, multiclass
    clus
vv   AMP PEAK  7(8P11.21) MUTATED AMP PEAK  7(8P11.21) WILD-TYPE
  R0                          173                            273
  R1                            2                              4
  R2                           22                             15
  RX                           16                             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
D7V13, binary
                                cls
clus                               0   1
  AMP PEAK  7(8P11.21) MUTATED     1 149
  AMP PEAK  7(8P11.21) WILD-TYPE   4 203
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8P11.21) MUTATED      1  149
  AMP PEAK  7(8P11.21) WILD-TYPE    4  203
                        clus
vv                       AMP PEAK  7(8P11.21) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          149
                        clus
vv                       AMP PEAK  7(8P11.21) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            203
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(8Q24.21) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  8(8Q24.21) MUTATED   271  82
  AMP PEAK  8(8Q24.21) WILD-TYPE 195  46
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                           353                            241 
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                            82                             46 
$`AMP PEAK  8(8Q24.21) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        13.94        24.16         1.02        24.03 
TCGA-AA-3524 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       36.03         0.99        13.02        23.01        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3867 TCGA-AA-3870 
       36.00        85.05        19.04        19.04        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       12.99        26.01        24.00        21.99        21.37        15.52 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 
      106.75         1.94        49.08         5.88        23.51        63.62 
TCGA-G4-6314 TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       35.93        10.39        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       26.43        15.62        12.66         1.61         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 
       43.76        43.76        43.43        35.11        16.57        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        36.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       29.19        23.61        32.71        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-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
       56.25         9.63         5.03         1.02        37.05        35.01 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        6.97         1.02        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3558 
       26.01        12.99        14.01        33.99        24.00        20.98 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 
       78.08         6.97        54.02        14.01        50.04        47.01 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3841 
       15.02         5.98        37.05         5.03        10.06        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       37.02        17.03        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       31.07        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 
       20.98        34.03         2.01        16.08        34.06        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00K TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A017 
       13.94        19.00        18.05         0.99        17.03        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A029 
       10.98        12.00        31.00         1.02        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AD-5900 
        2.96         2.01         5.03         0.92        41.00        12.16 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 
        5.79        22.42        27.42        26.47        16.44         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK 
       27.09        16.31         0.20        21.44        17.26        18.84 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
      109.28         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 
       11.74         3.19        12.69        12.36        12.46        12.59 
TCGA-CA-6715 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CK-5913 
       12.59        10.06        14.30       148.01        15.62        51.32 
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        25.02         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       27.02        13.02        29.06        22.98        30.08        32.02 
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-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       14.04        29.03        21.99        14.99        12.99        13.02 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       11.08        10.06        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 
       20.19        25.48        43.27        15.12         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 
       12.49        16.14        15.58         7.53        10.13        12.43 
TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       14.30         9.04        13.41        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA 
       24.43        38.20       130.65        49.91       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
       44.32        35.97        60.79       117.07        98.24         8.61 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6807 
       31.96        35.74        35.74         6.18        34.42        43.04 
TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
        8.35        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 
       55.04        39.42        36.00        26.43        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX 
       18.18        10.98        15.65        16.80        29.46        32.98 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
        8.42        38.70        70.03        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 
       43.04        13.55        34.49        37.74        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 
       86.63        65.98        36.03        32.02        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
        1.02        46.03        34.03        34.03         2.01        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
        6.05         0.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 
        0.99        19.04         1.02        36.95         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-4021 TCGA-AG-4022 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
        3.98        46.03        23.01        37.02         9.07         1.02 
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        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 
       43.20        27.55         6.05        13.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        21.01        25.05        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       13.97        31.00        51.98        10.98        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 
        4.18        17.00        15.85        16.34        16.31        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       10.78        13.64         9.96        49.51        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       32.19        37.18        11.87        12.46        47.08 

$`AMP PEAK  8(8Q24.21) WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 
       14.53        58.03        13.02        37.05         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3844 
       34.03        17.95        19.99         0.92        19.00        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3986 TCGA-AA-A00L 
       31.07        24.00         2.01        50.99        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 
       39.06        25.08        10.88        75.95       100.01        28.21 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-A015 TCGA-4N-A93T TCGA-A6-2672 TCGA-A6-2676 
        8.02        13.94        36.03         4.80        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5659 TCGA-A6-5661 
       42.28        44.91        37.05        32.75        30.44        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 
       22.09        22.06        22.52         8.38        21.76        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-AA-3489 
       20.12        19.66        16.24        24.92        61.84         7.04 
TCGA-AA-3492 TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3549 
        3.02        63.98        38.99         1.02         9.07        21.01 
TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3666 TCGA-AA-3675 TCGA-AA-3680 
       29.95        13.94        61.02         2.01        47.05        11.01 
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-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3855 
       15.95        38.99         0.00        10.06         0.00        32.05 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3968 TCGA-AA-3973 
       53.00        31.00        33.01        26.01        21.99        13.05 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00F 
       25.02         7.96        27.02        38.04        30.02        34.03 
TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A010 
       18.05         4.01        27.02        42.02        14.99        34.98 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       15.02        32.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A02Y 
       33.04         1.02        26.01        39.98        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 TCGA-AD-6890 TCGA-AM-5820 TCGA-AU-3779 
       18.05        40.96        83.24        24.53         0.46        14.50 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 
        0.95        33.01        17.82        17.85        19.33        58.39 
TCGA-AZ-4323 TCGA-AZ-6599 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 
        1.41         6.77        12.39        12.20        12.76        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       85.45        70.16        21.14        82.95       124.27        23.05 
TCGA-CM-4748 TCGA-CM-5344 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6171 
       26.04        22.03        12.00        16.04        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 
       11.01        12.95        13.05        11.08        11.01        12.03 
TCGA-D5-5537 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6920 
       45.40        20.42        17.75        18.25        17.85        12.39 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D4 TCGA-DM-A1D7 
        9.44        11.64        13.35        12.00        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       12.59       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6703 
       26.47        81.37       119.93        95.18        11.11        47.87 
TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        41.42        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 
       35.31       133.18        82.39        85.48        61.91        26.04 
TCGA-G4-6323 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV 
       13.78        19.33        19.33         9.93        12.79        42.77 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2693 TCGA-AF-4110 
       31.30        21.90        60.13        11.90        37.97        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 
       16.83        24.36        11.84        12.00         7.07        20.05 
TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 
       34.03        12.03        15.95        19.99        20.98        29.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99        17.95        13.02        35.01        14.01 
TCGA-AG-3901 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A020 TCGA-AG-A025 
       25.02        20.98        13.94         6.02         1.02        49.97 
TCGA-AG-A02G TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-DC-5337 
       38.96        26.43        19.46        33.17        44.78        26.04 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 
       44.02        25.97        12.62       129.27        51.48        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 
       19.96        20.91        18.28        17.69        16.41         8.61 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 
       17.46        11.97         8.45        42.35        36.49        19.66 
TCGA-F5-6861 
       38.14 

  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                             0                              0 
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                        148.01                         139.17 
  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE 
                         23.01                          21.14 
[1] "0.0 - 148.0 (23.0)" "0.0 - 139.2 (21.1)"
[1] "hr=" "1.3"
D8V2, continuous
D8V3, binary
                                cls
clus                               0   1
  AMP PEAK  8(8Q24.21) MUTATED   258 107
  AMP PEAK  8(8Q24.21) WILD-TYPE 190  55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.21) MUTATED    258  107
  AMP PEAK  8(8Q24.21) WILD-TYPE  190   55
        clus
vv       AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  COLON                           258                            190
  RECTUM                          107                             55
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  8(8Q24.21) MUTATED        56        0       25        96         4
  AMP PEAK  8(8Q24.21) WILD-TYPE      48        1       12        76         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  8(8Q24.21) MUTATED           2        11         12         49
  AMP PEAK  8(8Q24.21) WILD-TYPE         0        13          3         35
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  8(8Q24.21) MUTATED           35       48        16         0
  AMP PEAK  8(8Q24.21) WILD-TYPE         20       15         8         2
D8V4, multiclass
            clus
vv           AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  STAGE I                              56                             48
  STAGE IA                              0                              1
  STAGE II                             25                             12
  STAGE IIA                            96                             76
  STAGE IIB                             4                              8
  STAGE IIC                             2                              0
  STAGE III                            11                             13
  STAGE IIIA                           12                              3
  STAGE IIIB                           49                             35
  STAGE IIIC                           35                             20
  STAGE IV                             48                             15
  STAGE IVA                            16                              8
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  8(8Q24.21) MUTATED     8  62 256  38
  AMP PEAK  8(8Q24.21) WILD-TYPE  12  43 161  31
D8V5, multiclass
    clus
vv   AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  T1                            8                             12
  T2                           62                             43
  T3                          256                            161
  T4                           38                             31
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK  8(8Q24.21) MUTATED   199  86  78
  AMP PEAK  8(8Q24.21) WILD-TYPE 147  64  37
D8V6, multiclass
    clus
vv   AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  N0                          199                            147
  N1                           86                             64
  N2                           78                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                cls
clus                               0   1
  AMP PEAK  8(8Q24.21) MUTATED   258  64
  AMP PEAK  8(8Q24.21) WILD-TYPE 195  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.21) MUTATED    258   64
  AMP PEAK  8(8Q24.21) WILD-TYPE  195   24
   clus
vv  AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  0                          258                            195
  1                           64                             24
[1] 2 2
[1] FALSE
D8V8, binary
                                cls
clus                               0   1
  AMP PEAK  8(8Q24.21) MUTATED   164 202
  AMP PEAK  8(8Q24.21) WILD-TYPE 125 123
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.21) MUTATED    164  202
  AMP PEAK  8(8Q24.21) WILD-TYPE  125  123
        clus
vv       AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  FEMALE                          164                            125
  MALE                            202                            123
[1] 2 2
[1] FALSE
D8V9, binary
                                cls
clus                               0   1
  AMP PEAK  8(8Q24.21) MUTATED   281  17
  AMP PEAK  8(8Q24.21) WILD-TYPE 201  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.21) MUTATED    281   17
  AMP PEAK  8(8Q24.21) WILD-TYPE  201   12
     clus
vv    AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  NO                           281                            201
  YES                           17                             12
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  8(8Q24.21) MUTATED                    228
  AMP PEAK  8(8Q24.21) WILD-TYPE                  154
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(8Q24.21) MUTATED                              28
  AMP PEAK  8(8Q24.21) WILD-TYPE                            34
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK  8(8Q24.21) MUTATED                     100
  AMP PEAK  8(8Q24.21) WILD-TYPE                    46
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  8(8Q24.21) MUTATED                                5
  AMP PEAK  8(8Q24.21) WILD-TYPE                              8
D8V10, multiclass
                                clus
vv                               AMP PEAK  8(8Q24.21) MUTATED
  COLON ADENOCARCINOMA                                    228
  COLON MUCINOUS ADENOCARCINOMA                            28
  RECTAL ADENOCARCINOMA                                   100
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK  8(8Q24.21) WILD-TYPE
  COLON ADENOCARCINOMA                                      154
  COLON MUCINOUS ADENOCARCINOMA                              34
  RECTAL ADENOCARCINOMA                                      46
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  8(8Q24.21) MUTATED   255   4  28  19
  AMP PEAK  8(8Q24.21) WILD-TYPE 191   2   9  10
D8V11, multiclass
    clus
vv   AMP PEAK  8(8Q24.21) MUTATED AMP PEAK  8(8Q24.21) WILD-TYPE
  R0                          255                            191
  R1                            4                              2
  R2                           28                              9
  RX                           19                             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"
D8V12, continuous
D8V13, binary
                                cls
clus                               0   1
  AMP PEAK  8(8Q24.21) MUTATED     3 216
  AMP PEAK  8(8Q24.21) WILD-TYPE   2 136
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.21) MUTATED      3  216
  AMP PEAK  8(8Q24.21) WILD-TYPE    2  136
                        clus
vv                       AMP PEAK  8(8Q24.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          216
                        clus
vv                       AMP PEAK  8(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            136
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(10Q22.3) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(10Q22.3) MUTATED    28   9
  AMP PEAK  9(10Q22.3) WILD-TYPE 438 119
  AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE 
                            37                            557 
  AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE 
                             9                            119 
$`AMP PEAK  9(10Q22.3) MUTATED`
TCGA-A6-6649 TCGA-AA-3952 TCGA-DM-A285 TCGA-G4-6314 TCGA-BM-6198 TCGA-4T-AA8H 
       24.16         2.01         5.88        35.93        21.24        12.66 
TCGA-5M-AAT4 TCGA-AA-3666 TCGA-AA-3851 TCGA-AA-3869 TCGA-AA-3982 TCGA-AA-A01Q 
        1.61         2.01        33.07        27.02        27.02         1.02 
TCGA-AA-A01R TCGA-AY-A54L TCGA-CM-5860 TCGA-CM-6163 TCGA-CM-6678 TCGA-D5-5539 
       35.01        17.26        32.02        14.04        11.01        19.59 
TCGA-D5-6922 TCGA-D5-6924 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       10.13        14.30        13.32        12.59       140.38         7.50 
TCGA-DM-A1HA TCGA-G4-6299 TCGA-G4-6317 TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-A56K 
      131.51        74.56        36.00        21.90        39.48        86.63 
TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3881 TCGA-AG-3999 TCGA-AG-A020 TCGA-CI-6619 
       46.03        50.04        19.04        28.04         1.02         6.05 
TCGA-DC-4745 
       21.01 

$`AMP PEAK  9(10Q22.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.04        19.04        14.93        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        23.51        63.62        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 
       91.79        79.69        17.85        10.39         8.02        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
       19.99        17.03        17.03        25.97        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       31.00        51.98        18.28        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        4.80         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
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-A6-6650 
       22.52        24.13         8.38        25.08        25.18        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        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        5.03         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       37.02         0.00        17.03        10.06         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
       36.03        32.05         0.99        31.07        53.00        17.03 
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-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-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        25.02         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-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        33.04         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       26.47        16.44         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        33.01         0.20        21.44        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         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        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
        5.03        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 
       29.03        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.08        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6926 
       16.14        15.58         7.53        12.39        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        13.35        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-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       49.91        44.32       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-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18         8.35        82.39        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        31.30        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       60.13        11.90        70.03        46.92        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       24.36        20.02        24.59        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
        1.02        34.03        34.03        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       14.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
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 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       33.17        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.17        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       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         3.48         4.18        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        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE 
                          1.02                           0.00 
  AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE 
                        140.38                         148.01 
  AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE 
                         21.01                          22.06 
[1] "1.0 - 140.4 (21.0)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.1"
D9V2, continuous
D9V3, binary
                                cls
clus                               0   1
  AMP PEAK  9(10Q22.3) MUTATED    29  11
  AMP PEAK  9(10Q22.3) WILD-TYPE 419 151
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(10Q22.3) MUTATED     29   11
  AMP PEAK  9(10Q22.3) WILD-TYPE  419  151
        clus
vv       AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE
  COLON                            29                            419
  RECTUM                           11                            151
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK  9(10Q22.3) MUTATED         5        0        2         9         0
  AMP PEAK  9(10Q22.3) WILD-TYPE      99        1       35       163        12
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK  9(10Q22.3) MUTATED           0         4          2          4
  AMP PEAK  9(10Q22.3) WILD-TYPE         2        20         13         80
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK  9(10Q22.3) MUTATED            6        6         1         0
  AMP PEAK  9(10Q22.3) WILD-TYPE         49       57        23         2
D9V4, multiclass
            clus
vv           AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE
  STAGE I                               5                             99
  STAGE IA                              0                              1
  STAGE II                              2                             35
  STAGE IIA                             9                            163
  STAGE IIB                             0                             12
  STAGE IIC                             0                              2
  STAGE III                             4                             20
  STAGE IIIA                            2                             13
  STAGE IIIB                            4                             80
  STAGE IIIC                            6                             49
  STAGE IV                              6                             57
  STAGE IVA                             1                             23
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  9(10Q22.3) MUTATED     1   4  33   2
  AMP PEAK  9(10Q22.3) WILD-TYPE  19 101 384  67
D9V5, multiclass
    clus
vv   AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE
  T1                            1                             19
  T2                            4                            101
  T3                           33                            384
  T4                            2                             67
[1] 4 2
[1] TRUE
[1] "dimension 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(10Q22.3) MUTATED    17  11  12
  AMP PEAK  9(10Q22.3) WILD-TYPE 329 139 103
D9V6, multiclass
    clus
vv   AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE
  N0                           17                            329
  N1                           11                            139
  N2                           12                            103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                                cls
clus                               0   1
  AMP PEAK  9(10Q22.3) MUTATED    27   7
  AMP PEAK  9(10Q22.3) WILD-TYPE 426  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(10Q22.3) MUTATED     27    7
  AMP PEAK  9(10Q22.3) WILD-TYPE  426   81
   clus
vv  AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE
  0                           27                            426
  1                            7                             81
[1] 2 2
[1] FALSE
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(10Q22.3) MUTATED    17  23
  AMP PEAK  9(10Q22.3) WILD-TYPE 272 302
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(10Q22.3) MUTATED     17   23
  AMP PEAK  9(10Q22.3) WILD-TYPE  272  302
        clus
vv       AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE
  FEMALE                           17                            272
  MALE                             23                            302
[1] 2 2
[1] FALSE
D9V9, binary
                                cls
clus                               0   1
  AMP PEAK  9(10Q22.3) MUTATED    24   2
  AMP PEAK  9(10Q22.3) WILD-TYPE 458  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(10Q22.3) MUTATED     24    2
  AMP PEAK  9(10Q22.3) WILD-TYPE  458   27
     clus
vv    AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE
  NO                            24                            458
  YES                            2                             27
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK  9(10Q22.3) MUTATED                     24
  AMP PEAK  9(10Q22.3) WILD-TYPE                  358
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(10Q22.3) MUTATED                               4
  AMP PEAK  9(10Q22.3) WILD-TYPE                            58
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK  9(10Q22.3) MUTATED                       9
  AMP PEAK  9(10Q22.3) WILD-TYPE                   137
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK  9(10Q22.3) MUTATED                                1
  AMP PEAK  9(10Q22.3) WILD-TYPE                             12
D9V10, multiclass
                                clus
vv                               AMP PEAK  9(10Q22.3) MUTATED
  COLON ADENOCARCINOMA                                     24
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                     9
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK  9(10Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      358
  COLON MUCINOUS ADENOCARCINOMA                              58
  RECTAL ADENOCARCINOMA                                     137
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  9(10Q22.3) MUTATED    27   0   1   1
  AMP PEAK  9(10Q22.3) WILD-TYPE 419   6  36  28
D9V11, multiclass
    clus
vv   AMP PEAK  9(10Q22.3) MUTATED AMP PEAK  9(10Q22.3) WILD-TYPE
  R0                           27                            419
  R1                            0                              6
  R2                            1                             36
  RX                            1                             28
[1] 4 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
D9V13, binary
                                cls
clus                               0   1
  AMP PEAK  9(10Q22.3) MUTATED     1  23
  AMP PEAK  9(10Q22.3) WILD-TYPE   4 329
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(10Q22.3) MUTATED      1   23
  AMP PEAK  9(10Q22.3) WILD-TYPE    4  329
                        clus
vv                       AMP PEAK  9(10Q22.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           23
                        clus
vv                       AMP PEAK  9(10Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            329
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(11P15.5) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(11P15.5) MUTATED   105  28
  AMP PEAK 10(11P15.5) WILD-TYPE 361 100
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                           133                            461 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                            28                            100 
$`AMP PEAK 10(11P15.5) MUTATED`
TCGA-AA-3506 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        24.03        19.07        34.03        13.02        23.01 
TCGA-AA-3562 TCGA-AA-3867 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-6608 
       19.99        24.03        19.07        21.99        15.52         1.94 
TCGA-G4-6310 TCGA-G4-6314 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       63.62        35.93        10.39         8.02        13.94        19.99 
TCGA-AG-A00H TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 TCGA-A6-2671 TCGA-A6-2675 
       25.97        31.00        21.24        18.28        43.76        43.43 
TCGA-A6-2679 TCGA-A6-5660 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A5ZU 
       44.91        29.19        25.08        25.18        23.87         9.63 
TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3519 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3542 
        5.03         1.02         9.07         0.00        29.00        12.99 
TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3696 TCGA-AA-3819 
       24.00        13.94        50.04        47.01         5.03        25.02 
TCGA-AA-3831 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3875 
       17.98        37.02        17.03        33.07         0.99        18.05 
TCGA-AA-3955 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A01D TCGA-AA-A01S 
       20.98        27.02        34.03        17.03        10.98         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02J TCGA-AD-6901 TCGA-AM-5820 
        1.02        26.01        39.98         5.03        22.42         0.46 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 
       16.31         0.95        18.84        65.00        62.79        29.56 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
        3.19        12.46        12.59        12.20        14.30       148.01 
TCGA-CM-4750 TCGA-CM-5349 TCGA-CM-5868 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6677 
        8.02        30.08        17.03        29.03        21.99        11.08 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6929 
       54.61        56.09        25.48        17.85         7.53        13.41 
TCGA-DM-A1D6 TCGA-DM-A28F TCGA-DM-A28G TCGA-F4-6460 TCGA-F4-6463 TCGA-G4-6295 
       49.91        35.97        60.79        31.96        35.74         8.35 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-RU-A8FL 
       74.56        65.85        55.04        42.77        29.46        38.70 
TCGA-SS-A7HO TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-5654 TCGA-AF-6655 
       60.13        39.48        17.23        13.55        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3583 TCGA-AG-3587 
       24.59        65.98        36.03        12.00        20.05        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3894 
       34.03        34.03        34.03        19.99         0.99        14.01 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AH-6897 TCGA-CI-6621 TCGA-CI-6623 TCGA-DC-4749 
       36.03         1.02        26.43        13.78        47.44        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA 
       26.04        31.00        12.00        51.98        44.02       126.44 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6514 TCGA-F5-6810 TCGA-F5-6811 
        3.48         4.18        20.55        16.31         0.39        32.19 
TCGA-F5-6861 
       38.14 

$`AMP PEAK 10(11P15.5) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        37.05        36.03         8.05         0.99        17.95 
TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99         6.05         0.92        19.00        36.00        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        31.07        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L 
       24.00         2.01        50.99        26.01        24.00        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       39.06        21.37        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6321 
      100.01        49.08         5.88        28.21        23.51        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3890 
       35.80        26.17        91.79        79.69        17.85        17.03 
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 
       17.03        15.95        36.03        51.98        55.76        26.43 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 
       46.65        43.76        42.90        42.28        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        31.63        30.44        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-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       24.13         8.38        20.61        21.76        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
       56.25         7.04         3.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3532 
        6.97         1.02        38.99         1.02        19.07        29.00 
TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 
       26.01        14.01        33.99        21.01        29.95        20.98 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3710 
       47.05        15.02        11.01         5.98        37.05        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3833 TCGA-AA-3837 
       10.06        35.05         0.99         1.02        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       36.95         0.00        10.06         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 
       32.05        31.07        53.00        17.03        27.02        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 
        2.01        24.00        33.01        26.01        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 
       21.99        16.08        13.05        34.06        25.02         7.96 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       18.05         4.01        27.02        42.02         0.99        14.99 
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-A01T TCGA-AA-A01Z 
       31.00        38.07         1.02        35.01        33.04        37.02 
TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       51.98         2.96         2.01         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 
        5.79        27.42        26.47        16.44         0.92        14.50 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.85        19.33       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94         5.13        22.36        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
       12.10         5.23        11.74        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.59        12.76        10.06        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         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        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 
       27.02        13.02        29.06        22.03        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 
       15.02         5.03        15.02        15.02        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       14.04        16.04        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-6678 
       14.04        11.01        12.95        13.05        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        45.40        19.59        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 
       20.42        17.75        18.25        43.27        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
       12.43        14.30         9.04         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-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-A288 
       44.32       131.51       135.65         7.76       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       26.47        81.37       119.93       117.07        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        11.11        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 
       47.41        35.31       133.18        82.39        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       44.68        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        11.90        70.03 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       46.92        43.04        37.97        34.49        37.74        29.98 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       24.36        86.63        11.84        32.02         7.07        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       24.00         1.02         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        20.98         7.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        13.02        35.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 
       25.02        32.02        19.99        28.04        14.04         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        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        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       27.55        19.46         6.05        33.17        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
       78.12         7.17        21.01        13.97        31.00        10.98 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05        12.62        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 
      129.27        24.13        51.48        32.61        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        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-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-F5-6812 
        8.45         9.96        49.51        42.35        28.57        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        11.87        12.46        47.08 

  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                             0                              0 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE 
                         23.01                          21.99 
[1] "0.0 - 148.0 (23.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1"  
D10V2, continuous
D10V3, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED    90  44
  AMP PEAK 10(11P15.5) WILD-TYPE 358 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED     90   44
  AMP PEAK 10(11P15.5) WILD-TYPE  358  118
        clus
vv       AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  COLON                            90                            358
  RECTUM                           44                            118
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 10(11P15.5) MUTATED        20        0        6        35         3
  AMP PEAK 10(11P15.5) WILD-TYPE      84        1       31       137         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(11P15.5) MUTATED           0         6          4         17
  AMP PEAK 10(11P15.5) WILD-TYPE         2        18         11         67
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 10(11P15.5) MUTATED           14       18         7         0
  AMP PEAK 10(11P15.5) WILD-TYPE         41       45        17         2
D10V4, multiclass
            clus
vv           AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  STAGE I                              20                             84
  STAGE IA                              0                              1
  STAGE II                              6                             31
  STAGE IIA                            35                            137
  STAGE IIB                             3                              9
  STAGE IIC                             0                              2
  STAGE III                             6                             18
  STAGE IIIA                            4                             11
  STAGE IIIB                           17                             67
  STAGE IIIC                           14                             41
  STAGE IV                             18                             45
  STAGE IVA                             7                             17
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 10(11P15.5) MUTATED     6  23  96  10
  AMP PEAK 10(11P15.5) WILD-TYPE  14  82 321  59
D10V5, multiclass
    clus
vv   AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  T1                            6                             14
  T2                           23                             82
  T3                           96                            321
  T4                           10                             59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 10(11P15.5) MUTATED    70  35  30
  AMP PEAK 10(11P15.5) WILD-TYPE 276 115  85
D10V6, multiclass
    clus
vv   AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  N0                           70                            276
  N1                           35                            115
  N2                           30                             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"
D10V7, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED    98  24
  AMP PEAK 10(11P15.5) WILD-TYPE 355  64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED     98   24
  AMP PEAK 10(11P15.5) WILD-TYPE  355   64
   clus
vv  AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  0                           98                            355
  1                           24                             64
[1] 2 2
[1] FALSE
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED    66  70
  AMP PEAK 10(11P15.5) WILD-TYPE 223 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED     66   70
  AMP PEAK 10(11P15.5) WILD-TYPE  223  255
        clus
vv       AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  FEMALE                           66                            223
  MALE                             70                            255
[1] 2 2
[1] FALSE
D10V9, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED   110   7
  AMP PEAK 10(11P15.5) WILD-TYPE 372  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED    110    7
  AMP PEAK 10(11P15.5) WILD-TYPE  372   22
     clus
vv    AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  NO                           110                            372
  YES                            7                             22
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 10(11P15.5) MUTATED                     85
  AMP PEAK 10(11P15.5) WILD-TYPE                  297
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(11P15.5) MUTATED                               4
  AMP PEAK 10(11P15.5) WILD-TYPE                            58
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 10(11P15.5) MUTATED                      43
  AMP PEAK 10(11P15.5) WILD-TYPE                   103
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 10(11P15.5) MUTATED                                1
  AMP PEAK 10(11P15.5) WILD-TYPE                             12
D10V10, multiclass
                                clus
vv                               AMP PEAK 10(11P15.5) MUTATED
  COLON ADENOCARCINOMA                                     85
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 10(11P15.5) WILD-TYPE
  COLON ADENOCARCINOMA                                      297
  COLON MUCINOUS ADENOCARCINOMA                              58
  RECTAL ADENOCARCINOMA                                     103
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 10(11P15.5) MUTATED    97   1  10   7
  AMP PEAK 10(11P15.5) WILD-TYPE 349   5  27  22
D10V11, multiclass
    clus
vv   AMP PEAK 10(11P15.5) MUTATED AMP PEAK 10(11P15.5) WILD-TYPE
  R0                           97                            349
  R1                            1                              5
  R2                           10                             27
  RX                            7                             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"
D10V12, continuous
D10V13, binary
                                cls
clus                               0   1
  AMP PEAK 10(11P15.5) MUTATED     1  76
  AMP PEAK 10(11P15.5) WILD-TYPE   4 276
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11P15.5) MUTATED      1   76
  AMP PEAK 10(11P15.5) WILD-TYPE    4  276
                        clus
vv                       AMP PEAK 10(11P15.5) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           76
                        clus
vv                       AMP PEAK 10(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            276
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(12P13.33) MUTATION ANALYSIS
D11V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 11(12P13.33) MUTATED   112  34
  AMP PEAK 11(12P13.33) WILD-TYPE 354  94
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                            146                             448 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             34                              94 
$`AMP PEAK 11(12P13.33) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3560 TCGA-AA-3672 
       13.94        14.53        58.03        36.03        19.99         0.92 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AZ-6608 
       19.04        14.93        12.99        24.00         2.01         1.94 
TCGA-G4-6314 TCGA-AG-3611 TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6233 TCGA-G5-6641 
       35.93        13.94        15.95        36.03        18.28        26.43 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       15.62        12.66        44.91        37.02        34.65        32.75 
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-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3660 
        1.02         0.00        29.00        29.00        12.99        78.08 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3941 
        0.99        37.02         0.00        33.07         0.00        24.00 
TCGA-AA-3949 TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
       26.01        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        12.16 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 
       27.42        26.47         0.92        18.84         1.41         5.13 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CK-4948 
       49.41         6.77        11.74         3.19        12.36       148.01 
TCGA-CK-4950 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 
       85.45        15.62        51.32         2.01        20.02        25.02 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6166 TCGA-CM-6169 
       30.08        32.02        15.02        15.02        21.99        13.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6537 
       14.04        11.01        11.01        20.19        17.75         4.80 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6924 TCGA-D5-6928 TCGA-D5-6931 TCGA-D5-7000 
       12.49        15.58        14.30        11.64        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-F4-6809 TCGA-G4-6306 TCGA-G4-6323 TCGA-G4-6627 
       47.87        34.42        13.25        44.68        13.78        74.79 
TCGA-NH-A50U TCGA-NH-A6GB TCGA-QL-A97D TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       10.98        15.65        21.90        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 
       29.98        16.83        24.59        36.03        46.03         2.01 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3883 
        6.05        19.99         7.99        37.02        19.04         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A02G TCGA-AG-A02N 
       36.95         1.02        36.03        46.03        38.96        61.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       48.20        78.12        25.05        25.05        12.62       126.44 
TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
       57.24        32.61        19.96        18.28        17.69        13.64 
TCGA-EI-7002 TCGA-F5-6812 
       11.97        36.49 

$`AMP PEAK 11(12P13.33) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       37.05         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       17.95        23.01        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3972 
       85.05        19.04        31.07        24.03        29.98        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
      100.01        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-4N-A93T TCGA-5M-AAT4 
       31.00        51.98        21.24        55.76         4.80         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        35.11        16.57        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-A6-6651 TCGA-A6-6652 
       22.52        24.13         8.38        25.18        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A567 TCGA-A6-A56B 
       24.39        23.87        19.66        16.24        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
        9.63         5.03         7.04         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       19.07        26.01        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        61.02         6.97        54.02 
TCGA-AA-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-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       10.06        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 TCGA-AA-3855 
       36.95        17.03        10.06         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       31.00         2.01        33.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
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-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U 
       18.05         4.01        27.02        42.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       14.99        34.98        15.02        15.02        10.98        32.02 
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         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02W TCGA-AA-A03F TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       41.00        18.05        83.24        24.53         5.79        22.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
       16.44         0.46        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 
       33.01         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 
       19.33       109.28        58.39         5.65        32.94        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        88.21        12.10        29.56         5.23 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4951 TCGA-CK-5914 
       12.76        10.06        14.30        17.56        70.16        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
       21.14        82.95       124.27        23.05        37.02        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-5861 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02         5.03        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6674 
       29.03        16.04        14.99        12.99        15.02        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6540 
       25.48        43.27        15.12        17.85        17.13        16.14 
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-D5-6929 TCGA-D5-6930 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       13.41        13.35        11.38        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        12.59       140.38         7.50       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-A28H TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 
       35.97        60.79       117.07        98.24        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 
       35.74        35.74         6.18         1.55        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       33.67         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6307 
       82.39        74.56        67.30        65.85        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       85.48        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC 
       46.75        18.18        19.33        19.33         9.93        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       38.70        60.13        11.90        70.03        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       17.23        43.04        13.55        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00         1.02        34.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3727 
       50.04        12.03         0.99        15.95        20.98         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 
       29.98        32.98         0.99         0.99        19.99        17.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A002 
       19.99        28.04        14.04         1.02         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.02        49.97         1.94        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 
       33.17        13.78        44.78        47.44         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DE 
       51.98        10.98        44.02        25.97        41.36       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         3.48         4.18        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        15.85        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       42.35        28.57         0.39        32.19        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                              0                               0 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                         20.155                          22.470 
[1] "0.0 - 148.0 (20.2)" "0.0 - 140.4 (22.5)"
[1] "hr=" "1.2"
D11V2, continuous
D11V3, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED   112  39
  AMP PEAK 11(12P13.33) WILD-TYPE 336 123
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED    112   39
  AMP PEAK 11(12P13.33) WILD-TYPE  336  123
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  COLON                            112                             336
  RECTUM                            39                             123
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 11(12P13.33) MUTATED        23        1       13        49         3
  AMP PEAK 11(12P13.33) WILD-TYPE      81        0       24       123         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(12P13.33) MUTATED           0         5          4         11
  AMP PEAK 11(12P13.33) WILD-TYPE         2        19         11         73
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 11(12P13.33) MUTATED           16       15         8         0
  AMP PEAK 11(12P13.33) WILD-TYPE         39       48        16         2
D11V4, multiclass
            clus
vv           AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  STAGE I                               23                              81
  STAGE IA                               1                               0
  STAGE II                              13                              24
  STAGE IIA                             49                             123
  STAGE IIB                              3                               9
  STAGE IIC                              0                               2
  STAGE III                              5                              19
  STAGE IIIA                             4                              11
  STAGE IIIB                            11                              73
  STAGE IIIC                            16                              39
  STAGE IV                              15                              48
  STAGE IVA                              8                              16
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 11(12P13.33) MUTATED     2  28 102  20
  AMP PEAK 11(12P13.33) WILD-TYPE  18  77 315  49
D11V5, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  T1                             2                              18
  T2                            28                              77
  T3                           102                             315
  T4                            20                              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 11(12P13.33) MUTATED    95  29  29
  AMP PEAK 11(12P13.33) WILD-TYPE 251 121  86
D11V6, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  N0                            95                             251
  N1                            29                             121
  N2                            29                              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"
D11V7, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED   110  21
  AMP PEAK 11(12P13.33) WILD-TYPE 343  67
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED    110   21
  AMP PEAK 11(12P13.33) WILD-TYPE  343   67
   clus
vv  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  0                           110                             343
  1                            21                              67
[1] 2 2
[1] FALSE
D11V8, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED    72  81
  AMP PEAK 11(12P13.33) WILD-TYPE 217 244
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     72   81
  AMP PEAK 11(12P13.33) WILD-TYPE  217  244
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  FEMALE                            72                             217
  MALE                              81                             244
[1] 2 2
[1] FALSE
D11V9, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED   112  10
  AMP PEAK 11(12P13.33) WILD-TYPE 370  19
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED    112   10
  AMP PEAK 11(12P13.33) WILD-TYPE  370   19
     clus
vv    AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  NO                            112                             370
  YES                            10                              19
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 11(12P13.33) MUTATED                     95
  AMP PEAK 11(12P13.33) WILD-TYPE                  287
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(12P13.33) MUTATED                              16
  AMP PEAK 11(12P13.33) WILD-TYPE                            46
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 11(12P13.33) MUTATED                      33
  AMP PEAK 11(12P13.33) WILD-TYPE                   113
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 11(12P13.33) MUTATED                                5
  AMP PEAK 11(12P13.33) WILD-TYPE                              8
D11V10, multiclass
                                clus
vv                               AMP PEAK 11(12P13.33) MUTATED
  COLON ADENOCARCINOMA                                      95
  COLON MUCINOUS ADENOCARCINOMA                             16
  RECTAL ADENOCARCINOMA                                     33
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 11(12P13.33) WILD-TYPE
  COLON ADENOCARCINOMA                                       287
  COLON MUCINOUS ADENOCARCINOMA                               46
  RECTAL ADENOCARCINOMA                                      113
  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"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 11(12P13.33) MUTATED   110   2   6   7
  AMP PEAK 11(12P13.33) WILD-TYPE 336   4  31  22
D11V11, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  R0                           110                             336
  R1                             2                               4
  R2                             6                              31
  RX                             7                              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"
D11V12, continuous
D11V13, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED     0  89
  AMP PEAK 11(12P13.33) WILD-TYPE   5 263
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED      0   89
  AMP PEAK 11(12P13.33) WILD-TYPE    5  263
                        clus
vv                       AMP PEAK 11(12P13.33) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            89
                        clus
vv                       AMP PEAK 11(12P13.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             263
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(13Q12.13) MUTATION ANALYSIS
D12V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 12(13Q12.13) MUTATED   305  83
  AMP PEAK 12(13Q12.13) WILD-TYPE 161  45
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            388                             206 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                             83                              45 
$`AMP PEAK 12(13Q12.13) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3560 
       24.03        36.03        34.03         0.99        13.02        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
       19.99         6.05        19.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       31.07        24.03        29.98        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AD-6548 TCGA-AZ-4313 TCGA-AZ-4681 
       24.00        19.07        38.04        21.37        75.95       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 
       35.93        35.80        91.79        17.85        10.39        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
       19.99        17.03        17.03        25.97        15.95        36.03 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       51.98        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       12.66         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
       43.43        42.28        44.91        35.11        16.57        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       32.75        36.53        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-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13        25.08        25.18        20.61        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 
        7.04        37.05         6.97        38.99         9.07        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 
       24.00        20.98        13.94        78.08         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       50.04        15.02         5.98        37.05         5.03        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       35.05         0.99        25.02        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       10.06        32.05         0.99        31.07        17.03        27.02 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
        2.01        24.00        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       16.08        13.05        34.06        27.02         7.96        27.02 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 
       13.94        19.00        34.03        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        10.98        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-A54L 
       14.50        16.31         0.95        33.01        21.44        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       18.84       109.28         1.41         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        12.10        29.56         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 
       12.69        12.36        12.59        14.30        17.56       148.01 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       21.99         2.01        20.02        25.02         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        32.02         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        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 
       17.85         4.80        17.13        12.49         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 
       12.43        14.30         9.04        13.41        12.00        11.38 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 
       10.26       119.70       130.65        92.75        49.91        13.32 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
        7.50       131.51         7.76        14.04        26.47       119.93 
TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6570 TCGA-F4-6806 TCGA-F4-6807 
       35.97         8.61        31.96         6.18        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6295 
       33.67        13.25         0.53        47.41       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6317 
       82.39        74.56        65.85        44.68        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       26.43        46.75        74.79        18.18        19.33        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       16.80        42.77        29.46        32.98         8.42        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       38.70        60.13        11.90        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        7.07        36.03        20.05         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3725 
       34.03        34.03         2.01         0.99        19.99        20.98 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99        29.98         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       36.95        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03        14.04         1.02         3.98        46.03 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A025 TCGA-AG-A026 
        6.02        23.01        37.02         9.07        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.96        38.04        38.56        43.20        27.55        26.43 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       12.00        31.00        51.98        10.98        44.02        25.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       25.05       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         3.48         4.18        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 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        11.87        12.46        47.08 

$`AMP PEAK 12(13Q12.13) WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3554 
       24.33        13.02        37.05         8.05        19.07        17.95 
TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3952 
       23.01         0.92        36.00        19.04        24.00         2.01 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-6601 
       21.99        39.06        15.52        25.08        10.88       100.01 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-A01N TCGA-BM-6198 
       22.09        26.17        79.69         8.02        31.00        21.24 
TCGA-5M-AAT4 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-5657 
        1.61        42.90        37.05        37.25        37.02        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-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3555 TCGA-AA-3655 
        1.02         1.02        19.07         0.00        29.95        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3710 
        6.97        54.02        47.05        47.01        11.01        26.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 
        1.02        17.98        15.95        38.99         0.00         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 
       33.07         0.00        36.03        53.00        18.05        31.00 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       33.01         2.01        25.02        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 
       18.05         4.01        27.02         0.99        17.03        34.98 
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         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       26.01        37.02        51.98         5.03         0.92        22.03 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       18.05        12.16        83.24         0.46         0.92        27.09 
TCGA-AY-6196 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4614 
        0.20        17.82        17.85        19.33        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 
       32.94        88.21         6.77         3.19        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 
       12.59        12.20        12.76        10.06        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14        82.95       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        45.40 
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        13.35        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        35.74        35.74        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 
        1.55        34.42        35.31        67.30        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50U TCGA-NH-A5IV 
       85.48        61.91        26.04        13.78        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-3400 TCGA-AG-3574 
        9.93        12.79        31.30        70.03        34.49        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       12.00        32.02        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-3881 
       15.95         7.99        37.02        32.98         0.99        19.04 
TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J 
       13.02        48.03        25.02        20.98        13.94         1.02 
TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-DC-6155 
        1.02        61.97        41.00         2.50        19.46        13.97 
TCGA-DC-6681 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       25.97        12.62        19.96         8.61        13.64        17.46 
TCGA-F5-6814 TCGA-F5-6861 
       37.18        38.14 

  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                           0.39                            0.00 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                          22.47                           21.19 
[1] "0.4 - 148.0 (22.5)" "0.0 - 140.4 (21.2)"
[1] "hr=" "1"  
D12V2, continuous
D12V3, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED   274 123
  AMP PEAK 12(13Q12.13) WILD-TYPE 174  39
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED    274  123
  AMP PEAK 12(13Q12.13) WILD-TYPE  174   39
        clus
vv       AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  COLON                            274                             174
  RECTUM                           123                              39
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 12(13Q12.13) MUTATED        64        0       17        98         6
  AMP PEAK 12(13Q12.13) WILD-TYPE      40        1       20        74         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(13Q12.13) MUTATED           2        14         13         62
  AMP PEAK 12(13Q12.13) WILD-TYPE         0        10          2         22
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 12(13Q12.13) MUTATED           39       51        20         0
  AMP PEAK 12(13Q12.13) WILD-TYPE         16       12         4         2
D12V4, multiclass
            clus
vv           AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  STAGE I                               64                              40
  STAGE IA                               0                               1
  STAGE II                              17                              20
  STAGE IIA                             98                              74
  STAGE IIB                              6                               6
  STAGE IIC                              2                               0
  STAGE III                             14                              10
  STAGE IIIA                            13                               2
  STAGE IIIB                            62                              22
  STAGE IIIC                            39                              16
  STAGE IV                              51                              12
  STAGE IVA                             20                               4
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 12(13Q12.13) MUTATED    14  65 273  47
  AMP PEAK 12(13Q12.13) WILD-TYPE   6  40 144  22
D12V5, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  T1                            14                               6
  T2                            65                              40
  T3                           273                             144
  T4                            47                              22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 12(13Q12.13) MUTATED   198 113  87
  AMP PEAK 12(13Q12.13) WILD-TYPE 148  37  28
D12V6, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  N0                           198                             148
  N1                           113                              37
  N2                            87                              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"
D12V7, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED   284  70
  AMP PEAK 12(13Q12.13) WILD-TYPE 169  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED    284   70
  AMP PEAK 12(13Q12.13) WILD-TYPE  169   18
   clus
vv  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  0                           284                             169
  1                            70                              18
[1] 2 2
[1] FALSE
D12V8, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED   186 215
  AMP PEAK 12(13Q12.13) WILD-TYPE 103 110
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED    186  215
  AMP PEAK 12(13Q12.13) WILD-TYPE  103  110
        clus
vv       AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  FEMALE                           186                             103
  MALE                             215                             110
[1] 2 2
[1] FALSE
D12V9, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED   322  23
  AMP PEAK 12(13Q12.13) WILD-TYPE 160   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED    322   23
  AMP PEAK 12(13Q12.13) WILD-TYPE  160    6
     clus
vv    AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  NO                            322                             160
  YES                            23                               6
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 12(13Q12.13) MUTATED                    254
  AMP PEAK 12(13Q12.13) WILD-TYPE                  128
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(13Q12.13) MUTATED                              19
  AMP PEAK 12(13Q12.13) WILD-TYPE                            43
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 12(13Q12.13) MUTATED                     117
  AMP PEAK 12(13Q12.13) WILD-TYPE                    29
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 12(13Q12.13) MUTATED                                5
  AMP PEAK 12(13Q12.13) WILD-TYPE                              8
D12V10, multiclass
                                clus
vv                               AMP PEAK 12(13Q12.13) MUTATED
  COLON ADENOCARCINOMA                                     254
  COLON MUCINOUS ADENOCARCINOMA                             19
  RECTAL ADENOCARCINOMA                                    117
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 12(13Q12.13) WILD-TYPE
  COLON ADENOCARCINOMA                                       128
  COLON MUCINOUS ADENOCARCINOMA                               43
  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"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 12(13Q12.13) MUTATED   285   4  29  13
  AMP PEAK 12(13Q12.13) WILD-TYPE 161   2   8  16
D12V11, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  R0                           285                             161
  R1                             4                               2
  R2                            29                               8
  RX                            13                              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"
D12V12, continuous
D12V13, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED     4 238
  AMP PEAK 12(13Q12.13) WILD-TYPE   1 114
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED      4  238
  AMP PEAK 12(13Q12.13) WILD-TYPE    1  114
                        clus
vv                       AMP PEAK 12(13Q12.13) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           238
                        clus
vv                       AMP PEAK 12(13Q12.13) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             114
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(13Q12.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(13Q12.2) MUTATED   301  81
  AMP PEAK 13(13Q12.2) WILD-TYPE 165  47
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                           382                            212 
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                            81                             47 
$`AMP PEAK 13(13Q12.2) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3560 
       24.03        36.03        34.03         0.99        13.02        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
       19.99         6.05        19.00        85.05        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       31.07        24.03        29.98        12.99        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AD-6548 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6608 
       19.07        38.04        21.37        75.95       106.75         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 
       35.80        91.79        17.85        10.39        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 
       17.03        17.03        25.97        15.95        36.03        51.98 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       18.28        55.76        26.43        15.62         4.80        12.66 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 
       42.28        44.91        35.11        16.57        34.65        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.45        32.91        30.44        29.19        33.53        23.61 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 
       32.71        29.16        27.09        22.52        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       25.18        20.61        21.76        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3495 
       61.84        56.25         9.63         5.03         7.04        37.05 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        6.97        38.99         9.07        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       12.99        14.01        33.99        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3679 
       13.94        78.08         2.01        14.01        50.04        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3841 
        5.98        37.05        10.06        35.05         0.99        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       37.02        17.03        10.06        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 
       17.03        27.02         2.01        24.00        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
       34.03        21.99        16.08        13.05        34.06        27.02 
TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
        7.96        27.02        13.94        19.00        34.03        42.02 
TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       14.99        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W 
       31.00        33.04         2.96        39.98         2.01        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       39.98        40.96        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       26.47        16.44        14.50        16.31         0.95        33.01 
TCGA-AY-6197 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 
       21.44        17.26        18.84       109.28         1.41         5.13 
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-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 
        5.23        11.74        12.69        12.36        12.59        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 
       17.56       148.01        21.99         2.01        20.02        25.02 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 
       32.02         5.03        15.02        17.03        15.02        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 
       29.03        16.04        14.99        12.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5538 
       11.01        11.08        11.08        11.01        10.06        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 
        7.53        10.13        12.43        14.30         9.04        13.41 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D0 TCGA-DM-A1D4 
       12.00        11.38        10.26       119.70       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A280 TCGA-DM-A288 
       49.91        13.32         7.50       131.51         7.76        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        31.96         6.18 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 
      133.18         8.35        82.39        65.85        44.68        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       36.00        26.43        46.75        74.79        18.18        19.33 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       15.65        16.80        42.77        29.46        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 
       21.90        38.70        60.13        11.90        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 
       17.23        43.04        13.55        37.97        37.74        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        7.07        36.03        20.05         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3725 
       34.03        34.03         2.01         0.99        19.99        20.98 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99        29.98         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       36.95        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03        14.04         1.02         3.98        46.03 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A025 TCGA-AG-A026 
        6.02        23.01        37.02         9.07        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        38.56        43.20        27.55 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       26.43         6.05        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       12.00        31.00        51.98        10.98        44.02        25.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       25.05       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         3.48         4.18        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 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        11.87        12.46        47.08 

$`AMP PEAK 13(13Q12.2) WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3554 
       24.33        13.02        37.05         8.05        19.07        17.95 
TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3950 TCGA-AA-3952 
       23.01         0.92        36.00        19.04        24.00         2.01 
TCGA-AA-3979 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       24.00        21.99        39.06        15.52        25.08        10.88 
TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-A01N 
      100.01        22.09        26.17        79.69         8.02        31.00 
TCGA-BM-6198 TCGA-5M-AAT4 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       21.24         1.61        42.90        37.05        37.25        37.02 
TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 
       32.75        31.63        22.09        22.06         8.38        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 
       20.12        19.66        16.24        24.92         3.02         1.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
       35.01        63.98         1.02         1.02        19.07         0.00 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3678 
       29.95        61.02         6.97        54.02        47.05        47.01 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       11.01         5.03        26.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       15.95        38.99         0.00         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3966 
       36.03        53.00        18.05        31.00        33.01         2.01 
TCGA-AA-3977 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       25.02        38.04        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P 
       27.02         0.99        17.03        34.98        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         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-5900 
       51.98         5.03         0.92        22.03        18.05        12.16 
TCGA-AD-6889 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6386 
       83.24         0.46         0.92        27.09         0.20        17.82 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-5407 
       17.85        19.33        58.39         5.65        32.94        88.21 
TCGA-AZ-6599 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 
        6.77         3.19        12.46        12.39        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       12.76        10.06        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 
       21.14        82.95       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        45.40        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        13.35 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB 
       24.43        38.20        12.59       140.38        44.32       135.65 
TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
      139.17        81.37        60.79       117.07        98.24        95.18 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        35.74        35.74        47.87         1.55        34.42 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 
       35.31        74.56        67.30        53.62        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA 
       61.91        26.04        13.78        10.98        19.33         9.93 
TCGA-NH-A6GC TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 
       12.79        31.30        70.03        34.49        16.83        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       12.00        32.02        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-3881 
       15.95         7.99        37.02        32.98         0.99        19.04 
TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J 
       13.02        48.03        25.02        20.98        13.94         1.02 
TCGA-AG-A020 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 TCGA-DC-6155 
        1.02        61.97         2.50        19.46        33.17        13.97 
TCGA-DC-6681 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       25.97        12.62        19.96         8.61        13.64        17.46 
TCGA-F5-6814 TCGA-F5-6861 
       37.18        38.14 

  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                          0.39                           0.00 
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                        22.390                         21.615 
[1] "0.4 - 148.0 (22.4)" "0.0 - 140.4 (21.6)"
[1] "hr=" "1"  
D13V2, continuous
D13V3, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q12.2) MUTATED   269 122
  AMP PEAK 13(13Q12.2) WILD-TYPE 179  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q12.2) MUTATED    269  122
  AMP PEAK 13(13Q12.2) WILD-TYPE  179   40
        clus
vv       AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  COLON                           269                            179
  RECTUM                          122                             40
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 13(13Q12.2) MUTATED        64        0       17        96         5
  AMP PEAK 13(13Q12.2) WILD-TYPE      40        1       20        76         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(13Q12.2) MUTATED           2        14         13         62
  AMP PEAK 13(13Q12.2) WILD-TYPE         0        10          2         22
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 13(13Q12.2) MUTATED           38       50        19         0
  AMP PEAK 13(13Q12.2) WILD-TYPE         17       13         5         2
D13V4, multiclass
            clus
vv           AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  STAGE I                              64                             40
  STAGE IA                              0                              1
  STAGE II                             17                             20
  STAGE IIA                            96                             76
  STAGE IIB                             5                              7
  STAGE IIC                             2                              0
  STAGE III                            14                             10
  STAGE IIIA                           13                              2
  STAGE IIIB                           62                             22
  STAGE IIIC                           38                             17
  STAGE IV                             50                             13
  STAGE IVA                            19                              5
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 13(13Q12.2) MUTATED    14  65 268  46
  AMP PEAK 13(13Q12.2) WILD-TYPE   6  40 149  23
D13V5, multiclass
    clus
vv   AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  T1                           14                              6
  T2                           65                             40
  T3                          268                            149
  T4                           46                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 13(13Q12.2) MUTATED   195 111  86
  AMP PEAK 13(13Q12.2) WILD-TYPE 151  39  29
D13V6, multiclass
    clus
vv   AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  N0                          195                            151
  N1                          111                             39
  N2                           86                             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"
D13V7, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q12.2) MUTATED   280  68
  AMP PEAK 13(13Q12.2) WILD-TYPE 173  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q12.2) MUTATED    280   68
  AMP PEAK 13(13Q12.2) WILD-TYPE  173   20
   clus
vv  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  0                          280                            173
  1                           68                             20
[1] 2 2
[1] FALSE
D13V8, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q12.2) MUTATED   181 214
  AMP PEAK 13(13Q12.2) WILD-TYPE 108 111
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q12.2) MUTATED    181  214
  AMP PEAK 13(13Q12.2) WILD-TYPE  108  111
        clus
vv       AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  FEMALE                          181                            108
  MALE                            214                            111
[1] 2 2
[1] FALSE
D13V9, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q12.2) MUTATED   315  23
  AMP PEAK 13(13Q12.2) WILD-TYPE 167   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q12.2) MUTATED    315   23
  AMP PEAK 13(13Q12.2) WILD-TYPE  167    6
     clus
vv    AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  NO                           315                            167
  YES                           23                              6
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 13(13Q12.2) MUTATED                    250
  AMP PEAK 13(13Q12.2) WILD-TYPE                  132
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(13Q12.2) MUTATED                              18
  AMP PEAK 13(13Q12.2) WILD-TYPE                            44
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 13(13Q12.2) MUTATED                     116
  AMP PEAK 13(13Q12.2) WILD-TYPE                    30
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 13(13Q12.2) MUTATED                                5
  AMP PEAK 13(13Q12.2) WILD-TYPE                              8
D13V10, multiclass
                                clus
vv                               AMP PEAK 13(13Q12.2) MUTATED
  COLON ADENOCARCINOMA                                    250
  COLON MUCINOUS ADENOCARCINOMA                            18
  RECTAL ADENOCARCINOMA                                   116
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 13(13Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      132
  COLON MUCINOUS ADENOCARCINOMA                              44
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 13(13Q12.2) MUTATED   281   4  28  13
  AMP PEAK 13(13Q12.2) WILD-TYPE 165   2   9  16
D13V11, multiclass
    clus
vv   AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  R0                          281                            165
  R1                            4                              2
  R2                           28                              9
  RX                           13                             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"
D13V12, continuous
D13V13, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q12.2) MUTATED     4 234
  AMP PEAK 13(13Q12.2) WILD-TYPE   1 118
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q12.2) MUTATED      4  234
  AMP PEAK 13(13Q12.2) WILD-TYPE    1  118
                        clus
vv                       AMP PEAK 13(13Q12.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          234
                        clus
vv                       AMP PEAK 13(13Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            118
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(13Q22.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 14(13Q22.1) MUTATED   299  83
  AMP PEAK 14(13Q22.1) WILD-TYPE 167  45
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                           382                            212 
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                            83                             45 
$`AMP PEAK 14(13Q22.1) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3560 
       24.03        36.03        34.03         0.99        13.02        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3715 TCGA-AA-3844 
       19.99         6.05        19.00        85.05        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99         2.01        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4313 
       19.07        38.04        21.37        15.52        25.08        75.95 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6586 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 
       35.93        35.80        91.79        17.85        10.39        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
       19.99        17.03        17.03        25.97        15.95        36.03 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       51.98        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       12.66         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
       43.43        42.28        44.91        35.11        16.57        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       36.53        32.45        32.91        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       23.61        32.71        29.16        27.09        22.52        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        20.61        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3534 
       37.05         6.97        38.99         9.07        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3558 
       26.01        12.99        14.01        21.01        24.00        20.98 
TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       13.94        78.08        54.02         2.01        14.01        50.04 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       15.02         5.98        37.05        10.06        35.05         0.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3855 TCGA-AA-3856 
       36.95        37.02        17.03        10.06        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 
       31.07        17.03        27.02        18.05         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       26.01        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D 
       34.06        27.02         7.96        27.02        13.94        19.00 
TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C 
       34.03        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 
       10.98        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       16.44        14.50        16.31         0.95        33.01        21.44 
TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 
       17.26        18.84       109.28         1.41         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       65.00        62.79        49.41        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 
       11.74        12.69        12.36        12.59        14.30        17.56 
TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 
      148.01        21.99         2.01        20.02        25.02         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        32.02 
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        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 
       56.09        55.92        17.75        18.25        25.48        43.27 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 
       15.12        17.85         4.80        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-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-A1DA TCGA-DM-A1HA TCGA-DM-A280 
       92.75        49.91        13.32         7.50       131.51         7.76 
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        31.96         6.18 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
      133.18         8.35        82.39        74.56        65.85        44.68 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       39.42        36.00        26.43        46.75        74.79        18.18 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2687 
       32.98         8.42        21.90        38.70        60.13        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       39.48        17.23        43.04        13.55        37.97        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       29.98        24.36        20.02        24.59        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       11.84         7.07        36.03        20.05         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3725 
       34.03        34.03        34.03         0.99        19.99        20.98 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99        29.98         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       36.95        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        46.03         6.02 
TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       23.01         9.07        49.97         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6621 
       38.56        43.20        27.55        26.43         6.05        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        12.00        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        44.02        25.05        25.05        12.62       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-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        3.48        20.55        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-7002 
       16.34        16.31        16.41        11.51        10.78        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
       36.49        19.66        11.87        47.08 

$`AMP PEAK 14(13Q22.1) WILD-TYPE`
TCGA-A6-2677 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3554 
       24.33        13.02        37.05         8.05        19.07        17.95 
TCGA-AA-3556 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3860 TCGA-AA-3950 
       23.01         0.92        36.00        19.04        31.07        24.00 
TCGA-AA-3979 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6601 
       24.00        21.99        39.06        10.88       106.75       100.01 
TCGA-G4-6321 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-A01N TCGA-BM-6198 
       22.09        26.17        79.69         8.02        31.00        21.24 
TCGA-5M-AAT4 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
        1.61        42.90        37.05        37.25        37.02        32.75 
TCGA-A6-5657 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       31.63        22.09        22.06         8.38        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3502 
       19.66        16.24        24.92         3.02         1.02        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3548 
       63.98         1.02         1.02        19.07         0.00        33.99 
TCGA-AA-3555 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       29.95        61.02         6.97        47.05        47.01        11.01 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
        5.03        26.99        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       38.99         0.00         0.00        33.07         0.00        36.03 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-A00A 
       53.00        31.00        33.01         2.01        25.02        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       30.02        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A010 TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V 
       34.98        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       26.01        37.02        51.98         5.03         0.92        22.03 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 
       18.05        83.24         0.46         0.92        27.09         0.20 
TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 
       17.82        17.85        19.33        58.39         5.65        32.94 
TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       88.21         6.77         3.19        12.46        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       12.20        12.76        10.06        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 
       51.32        21.14        82.95       124.27        23.05        37.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6162 TCGA-CM-6166 
       26.04        27.02        15.02        15.02        12.00        21.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 
       14.04        12.95        13.05        12.03        45.40        20.19 
TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       20.42        16.14        15.58        12.39         9.44        11.64 
TCGA-D5-6930 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A282 
       13.35        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-F4-6459 
       81.37        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       11.11        35.74        35.74        47.87         1.55        34.42 
TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6315 
       35.31        67.30        53.62        55.04        85.48        61.91 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GC TCGA-QG-A5Z2 
       26.04        13.78        10.98        19.33        12.79        31.30 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 
       11.90        70.03        34.49        16.83        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       32.02        24.00         2.01        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
       15.95         7.99        37.02        32.98         0.99        19.04 
TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 
       13.02        48.03        25.02         3.98        20.98        13.94 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       37.02         1.02         1.02        61.97        41.00         2.50 
TCGA-AH-6903 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6681 TCGA-EF-5831 TCGA-EI-6507 
       19.46        33.17        13.97        25.97         4.18        19.96 
TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 
       20.91         8.61        13.64        17.46         8.45        37.18 
TCGA-F5-6861 TCGA-F5-6864 
       38.14        12.46 

  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                          0.39                           0.00 
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                        22.390                         21.615 
[1] "0.4 - 148.0 (22.4)" "0.0 - 140.4 (21.6)"
[1] "hr=" "1.1"
D14V2, continuous
D14V3, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q22.1) MUTATED   276 117
  AMP PEAK 14(13Q22.1) WILD-TYPE 172  45
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q22.1) MUTATED    276  117
  AMP PEAK 14(13Q22.1) WILD-TYPE  172   45
        clus
vv       AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  COLON                           276                            172
  RECTUM                          117                             45
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 14(13Q22.1) MUTATED        65        0       21        92         5
  AMP PEAK 14(13Q22.1) WILD-TYPE      39        1       16        80         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 14(13Q22.1) MUTATED           2        15         13         61
  AMP PEAK 14(13Q22.1) WILD-TYPE         0         9          2         23
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 14(13Q22.1) MUTATED           41       49        19         0
  AMP PEAK 14(13Q22.1) WILD-TYPE         14       14         5         2
D14V4, multiclass
            clus
vv           AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  STAGE I                              65                             39
  STAGE IA                              0                              1
  STAGE II                             21                             16
  STAGE IIA                            92                             80
  STAGE IIB                             5                              7
  STAGE IIC                             2                              0
  STAGE III                            15                              9
  STAGE IIIA                           13                              2
  STAGE IIIB                           61                             23
  STAGE IIIC                           41                             14
  STAGE IV                             49                             14
  STAGE IVA                            19                              5
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 14(13Q22.1) MUTATED    15  65 269  46
  AMP PEAK 14(13Q22.1) WILD-TYPE   5  40 148  23
D14V5, multiclass
    clus
vv   AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  T1                           15                              5
  T2                           65                             40
  T3                          269                            148
  T4                           46                             23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  AMP PEAK 14(13Q22.1) MUTATED   196 113  85
  AMP PEAK 14(13Q22.1) WILD-TYPE 150  37  30
D14V6, multiclass
    clus
vv   AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  N0                          196                            150
  N1                          113                             37
  N2                           85                             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"
D14V7, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q22.1) MUTATED   281  67
  AMP PEAK 14(13Q22.1) WILD-TYPE 172  21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q22.1) MUTATED    281   67
  AMP PEAK 14(13Q22.1) WILD-TYPE  172   21
   clus
vv  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  0                          281                            172
  1                           67                             21
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q22.1) MUTATED   179 218
  AMP PEAK 14(13Q22.1) WILD-TYPE 110 107
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q22.1) MUTATED    179  218
  AMP PEAK 14(13Q22.1) WILD-TYPE  110  107
        clus
vv       AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  FEMALE                          179                            110
  MALE                            218                            107
[1] 2 2
[1] FALSE
D14V9, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q22.1) MUTATED   311  24
  AMP PEAK 14(13Q22.1) WILD-TYPE 171   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q22.1) MUTATED    311   24
  AMP PEAK 14(13Q22.1) WILD-TYPE  171    5
     clus
vv    AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  NO                           311                            171
  YES                           24                              5
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 14(13Q22.1) MUTATED                    255
  AMP PEAK 14(13Q22.1) WILD-TYPE                  127
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(13Q22.1) MUTATED                              19
  AMP PEAK 14(13Q22.1) WILD-TYPE                            43
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 14(13Q22.1) MUTATED                     112
  AMP PEAK 14(13Q22.1) WILD-TYPE                    34
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 14(13Q22.1) MUTATED                                4
  AMP PEAK 14(13Q22.1) WILD-TYPE                              9
D14V10, multiclass
                                clus
vv                               AMP PEAK 14(13Q22.1) MUTATED
  COLON ADENOCARCINOMA                                    255
  COLON MUCINOUS ADENOCARCINOMA                            19
  RECTAL ADENOCARCINOMA                                   112
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               AMP PEAK 14(13Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      127
  COLON MUCINOUS ADENOCARCINOMA                              43
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 14(13Q22.1) MUTATED   281   4  27  14
  AMP PEAK 14(13Q22.1) WILD-TYPE 165   2  10  15
D14V11, multiclass
    clus
vv   AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  R0                          281                            165
  R1                            4                              2
  R2                           27                             10
  RX                           14                             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
D14V13, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q22.1) MUTATED     4 235
  AMP PEAK 14(13Q22.1) WILD-TYPE   1 117
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q22.1) MUTATED      4  235
  AMP PEAK 14(13Q22.1) WILD-TYPE    1  117
                        clus
vv                       AMP PEAK 14(13Q22.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          235
                        clus
vv                       AMP PEAK 14(13Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            117
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(15Q26.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 15(15Q26.1) MUTATED    28  11
  AMP PEAK 15(15Q26.1) WILD-TYPE 438 117
  AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE 
                            39                            555 
  AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE 
                            11                            117 
$`AMP PEAK 15(15Q26.1) MUTATED`
TCGA-A6-6649 TCGA-AA-3560 TCGA-AG-3612 TCGA-BM-6198 TCGA-3L-AA1B TCGA-A6-2671 
       24.16        19.99        19.99        21.24        15.62        43.76 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3681 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3941 
       29.00        29.00         5.98        36.03         0.99        24.00 
TCGA-AA-A02H TCGA-AY-4070 TCGA-AY-6196 TCGA-AZ-4614 TCGA-CA-5254 TCGA-CM-5348 
        2.01        16.31         0.20         5.65        12.69        22.98 
TCGA-CM-5349 TCGA-CM-6161 TCGA-D5-6531 TCGA-D5-6538 TCGA-DM-A1DB TCGA-DM-A288 
       30.08        15.02        17.75        17.13        44.32        14.04 
TCGA-DM-A28A TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6626 TCGA-QG-A5YV TCGA-AF-3400 
       26.47        82.39        74.56        46.75        42.77        34.49 
TCGA-AG-3587 TCGA-AG-3609 TCGA-AH-6643 TCGA-CI-6623 TCGA-CL-5918 TCGA-DY-A1DC 
       46.03        19.99        43.20        47.44         7.17        41.36 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6864 
        8.45         9.96        12.46 

$`AMP PEAK 15(15Q26.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
        8.02        13.94        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       36.03        31.00        51.98        18.28        55.76        26.43 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
        4.80        12.66         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
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-A6-5664 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        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        9.07        19.07         0.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 
       50.04        47.05        47.01        15.02        11.01        37.05 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       32.05        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
       31.00         2.01        33.01        26.01        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
        2.01        21.99        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-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-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        10.98        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         1.02 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J 
       26.01        37.02        51.98         2.96        39.98         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        0.92        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       26.47        16.44         0.46         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       19.33        18.84       109.28        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 
        6.77        12.10        29.56         5.23        11.74         3.19 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.36        12.46        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
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        25.02 
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 
       32.02        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 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        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        13.35        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-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H 
      139.17        81.37       119.93        35.97        60.79       117.07 
TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
      133.18         8.35        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.04        13.78        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33         9.93        15.65        12.79        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO 
       32.98         8.42        31.30        21.90        38.70        60.13 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       13.55        37.97        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       19.99        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        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        38.56         2.50        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       48.20        78.12        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
       25.97        25.05        25.05        12.62       126.44        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         3.48         4.18 
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-F5-6465 TCGA-F5-6571 
       10.78        13.64        17.46        11.97        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       38.14        11.87        47.08 

  AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE 
                           0.2                            0.0 
  AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE 
                         82.39                         148.01 
  AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE 
                         21.24                          22.03 
[1] "0.2 - 82.4 (21.2)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D15V2, continuous
D15V3, binary
                                cls
clus                               0   1
  AMP PEAK 15(15Q26.1) MUTATED    29  13
  AMP PEAK 15(15Q26.1) WILD-TYPE 419 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(15Q26.1) MUTATED     29   13
  AMP PEAK 15(15Q26.1) WILD-TYPE  419  149
        clus
vv       AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE
  COLON                            29                            419
  RECTUM                           13                            149
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 15(15Q26.1) MUTATED         5        0        1        11         0
  AMP PEAK 15(15Q26.1) WILD-TYPE      99        1       36       161        12
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 15(15Q26.1) MUTATED           0         1          0          6
  AMP PEAK 15(15Q26.1) WILD-TYPE         2        23         15         78
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 15(15Q26.1) MUTATED           10        5         2         0
  AMP PEAK 15(15Q26.1) WILD-TYPE         45       58        22         2
D15V4, multiclass
            clus
vv           AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE
  STAGE I                               5                             99
  STAGE IA                              0                              1
  STAGE II                              1                             36
  STAGE IIA                            11                            161
  STAGE IIB                             0                             12
  STAGE IIC                             0                              2
  STAGE III                             1                             23
  STAGE IIIA                            0                             15
  STAGE IIIB                            6                             78
  STAGE IIIC                           10                             45
  STAGE IV                              5                             58
  STAGE IVA                             2                             22
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 15(15Q26.1) MUTATED     1   4  30   7
  AMP PEAK 15(15Q26.1) WILD-TYPE  19 101 387  62
D15V5, multiclass
    clus
vv   AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE
  T1                            1                             19
  T2                            4                            101
  T3                           30                            387
  T4                            7                             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
  AMP PEAK 15(15Q26.1) MUTATED    17   8  17
  AMP PEAK 15(15Q26.1) WILD-TYPE 329 142  98
D15V6, multiclass
    clus
vv   AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE
  N0                           17                            329
  N1                            8                            142
  N2                           17                             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                               0   1
  AMP PEAK 15(15Q26.1) MUTATED    31   7
  AMP PEAK 15(15Q26.1) WILD-TYPE 422  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(15Q26.1) MUTATED     31    7
  AMP PEAK 15(15Q26.1) WILD-TYPE  422   81
   clus
vv  AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE
  0                           31                            422
  1                            7                             81
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(15Q26.1) MUTATED    24  18
  AMP PEAK 15(15Q26.1) WILD-TYPE 265 307
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(15Q26.1) MUTATED     24   18
  AMP PEAK 15(15Q26.1) WILD-TYPE  265  307
        clus
vv       AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE
  FEMALE                           24                            265
  MALE                             18                            307
[1] 2 2
[1] FALSE
D15V9, binary
                                cls
clus                               0   1
  AMP PEAK 15(15Q26.1) MUTATED    29   2
  AMP PEAK 15(15Q26.1) WILD-TYPE 453  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(15Q26.1) MUTATED     29    2
  AMP PEAK 15(15Q26.1) WILD-TYPE  453   27
     clus
vv    AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE
  NO                            29                            453
  YES                            2                             27
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 15(15Q26.1) MUTATED                     25
  AMP PEAK 15(15Q26.1) WILD-TYPE                  357
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(15Q26.1) MUTATED                               4
  AMP PEAK 15(15Q26.1) WILD-TYPE                            58
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 15(15Q26.1) MUTATED                      11
  AMP PEAK 15(15Q26.1) WILD-TYPE                   135
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 15(15Q26.1) MUTATED                                2
  AMP PEAK 15(15Q26.1) WILD-TYPE                             11
D15V10, multiclass
                                clus
vv                               AMP PEAK 15(15Q26.1) MUTATED
  COLON ADENOCARCINOMA                                     25
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    11
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK 15(15Q26.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      357
  COLON MUCINOUS ADENOCARCINOMA                              58
  RECTAL ADENOCARCINOMA                                     135
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 15(15Q26.1) MUTATED    30   1   3   2
  AMP PEAK 15(15Q26.1) WILD-TYPE 416   5  34  27
D15V11, multiclass
    clus
vv   AMP PEAK 15(15Q26.1) MUTATED AMP PEAK 15(15Q26.1) WILD-TYPE
  R0                           30                            416
  R1                            1                              5
  R2                            3                             34
  RX                            2                             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"
D15V12, continuous
D15V13, binary
                                cls
clus                               0   1
  AMP PEAK 15(15Q26.1) MUTATED     0  27
  AMP PEAK 15(15Q26.1) WILD-TYPE   5 325
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(15Q26.1) MUTATED      0   27
  AMP PEAK 15(15Q26.1) WILD-TYPE    5  325
                        clus
vv                       AMP PEAK 15(15Q26.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           27
                        clus
vv                       AMP PEAK 15(15Q26.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            325
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(16P11.2) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(16P11.2) MUTATED   134  31
  AMP PEAK 16(16P11.2) WILD-TYPE 332  97
  AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE 
                           165                            429 
  AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE 
                            31                             97 
$`AMP PEAK 16(16P11.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 
       24.33        45.60        13.02        19.99        19.99        19.00 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3976 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6310 TCGA-G4-6314 TCGA-AF-3913 
       26.01         1.94        49.08        63.62        35.93        10.39 
TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 
       13.94        17.03        15.95        36.03        31.00        21.24 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       39.45        43.76        43.43        44.91        35.11        16.57 
TCGA-A6-2685 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6140 
       37.25        32.45        30.44        29.19        29.16        24.13 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6654 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
       25.08        20.61        23.87        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3812 TCGA-AA-3841 
       33.99        24.00        50.04        15.02        35.05        36.95 
TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3856 TCGA-AA-3866 
       37.02        17.03        33.07         0.00         0.99        17.03 
TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       27.02         2.01        24.00        20.98        34.03        16.08 
TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01G TCGA-AA-A01T 
       27.02        34.03        42.02        15.02        12.00        33.04 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4071 
       41.00        40.96        22.42        27.42        26.47         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-5403 
       33.01         0.20        17.26        18.84         5.13        62.79 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 
       29.56         5.23        12.69        12.59        14.30       148.01 
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 
       32.02        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        25.48 
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        31.96         1.55 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 
       82.39        74.56        65.85        44.68        55.04        39.42 
TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QL-A97D 
       26.43        13.78        46.75        15.65        12.79        21.90 
TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       11.90        39.48        37.74        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3726 
       65.98        36.03        34.03         6.05        20.98         7.99 
TCGA-AG-3731 TCGA-AG-3885 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 
       37.02        17.95        19.99        36.03         1.02        46.03 
TCGA-AG-A016 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6622 TCGA-CI-6623 
        9.07        38.96        38.04        27.55        44.78        47.44 
TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF 
       78.12        25.05        31.00        12.00        25.05        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 
       51.48         3.48        17.69        16.31        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
        0.39        32.19        11.87 

$`AMP PEAK 16(16P11.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 
        0.99        17.95        23.01         6.05         0.92        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3979 
       85.05        19.04        19.04        24.00        50.99        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-DM-A285 
       25.08        10.88        75.95       106.75       100.01         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       28.21        23.51        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H 
       79.69        17.85         8.02        19.99        17.03        25.97 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       51.98        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2676 
       12.66         1.61         9.53        46.65        43.76        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       42.28        37.05        37.02        34.65        32.75        36.53 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6651 
       32.71        27.09        22.52         8.38        25.18        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        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       29.00        14.01        21.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.05        47.01        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       26.99        10.06         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3854 
       15.95        38.99         0.00        10.06         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3947 
       32.05        31.07        53.00        18.05        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       26.01         2.01        21.99        13.05        34.06        25.02 
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-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I 
       14.99        34.98        15.02        10.98        32.02        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         1.02 
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-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        5.03         0.92        22.03        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       83.24        24.53         5.79        16.44         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D 
       14.50        27.09        16.31        21.44        17.82        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        65.00        88.21        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19        12.36        12.46        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.20        12.76        10.06        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5341 
       23.05        37.02        25.02        26.04        27.02        29.06 
TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 
       30.08        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 
       12.00        16.04        12.99        13.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 
       13.05        11.08        11.08        11.01        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       54.61        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       43.27        17.85         4.80        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        12.43        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-A1D0 
       13.35        12.00        10.26       119.70        24.43       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       92.75        49.91        12.59       140.38         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-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M 
       81.37       119.93        60.79       117.07        98.24        95.18 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 
       35.31       133.18         8.35        67.30        53.62        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       61.91        36.00        26.04        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33        19.33         9.93        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-WS-AB45 
       32.98         8.42        31.30        38.70        60.13        70.03 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       46.92        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       29.98        16.83        24.59        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       32.02         7.07        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       34.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 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-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99        19.04        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        14.04         3.98        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         1.02         1.02        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.97        41.00        38.56         2.50        43.20        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6624 TCGA-CL-5918 
       19.46         6.05        33.17        13.78        48.20         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       21.01        26.04        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       57.24       129.27        32.61         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
       20.91        17.00        18.28        15.85        16.34        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-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        8.45         9.96        42.35        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       38.14        12.46        47.08 

  AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE 
                             0                              0 
  AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE 
                         24.03                          21.01 
[1] "0.0 - 148.0 (24.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1.1"
D16V2, continuous
D16V3, binary
                                cls
clus                               0   1
  AMP PEAK 16(16P11.2) MUTATED   124  47
  AMP PEAK 16(16P11.2) WILD-TYPE 324 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(16P11.2) MUTATED    124   47
  AMP PEAK 16(16P11.2) WILD-TYPE  324  115
        clus
vv       AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE
  COLON                           124                            324
  RECTUM                           47                            115
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 16(16P11.2) MUTATED        20        1        4        37         3
  AMP PEAK 16(16P11.2) WILD-TYPE      84        0       33       135         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 16(16P11.2) MUTATED           0         7          8         30
  AMP PEAK 16(16P11.2) WILD-TYPE         2        17          7         54
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 16(16P11.2) MUTATED           22       23         8         1
  AMP PEAK 16(16P11.2) WILD-TYPE         33       40        16         1
D16V4, multiclass
            clus
vv           AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE
  STAGE I                              20                             84
  STAGE IA                              1                              0
  STAGE II                              4                             33
  STAGE IIA                            37                            135
  STAGE IIB                             3                              9
  STAGE IIC                             0                              2
  STAGE III                             7                             17
  STAGE IIIA                            8                              7
  STAGE IIIB                           30                             54
  STAGE IIIC                           22                             33
  STAGE IV                             23                             40
  STAGE IVA                             8                             16
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 16(16P11.2) MUTATED     5  26 122  17
  AMP PEAK 16(16P11.2) WILD-TYPE  15  79 295  52
D16V5, multiclass
    clus
vv   AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE
  T1                            5                             15
  T2                           26                             79
  T3                          122                            295
  T4                           17                             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
  AMP PEAK 16(16P11.2) MUTATED    72  55  43
  AMP PEAK 16(16P11.2) WILD-TYPE 274  95  72
D16V6, multiclass
    clus
vv   AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE
  N0                           72                            274
  N1                           55                             95
  N2                           43                             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"
D16V7, binary
                                cls
clus                               0   1
  AMP PEAK 16(16P11.2) MUTATED   116  32
  AMP PEAK 16(16P11.2) WILD-TYPE 337  56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(16P11.2) MUTATED    116   32
  AMP PEAK 16(16P11.2) WILD-TYPE  337   56
   clus
vv  AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE
  0                          116                            337
  1                           32                             56
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(16P11.2) MUTATED    81  91
  AMP PEAK 16(16P11.2) WILD-TYPE 208 234
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(16P11.2) MUTATED     81   91
  AMP PEAK 16(16P11.2) WILD-TYPE  208  234
        clus
vv       AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE
  FEMALE                           81                            208
  MALE                             91                            234
[1] 2 2
[1] FALSE
D16V9, binary
                                cls
clus                               0   1
  AMP PEAK 16(16P11.2) MUTATED   140   9
  AMP PEAK 16(16P11.2) WILD-TYPE 342  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(16P11.2) MUTATED    140    9
  AMP PEAK 16(16P11.2) WILD-TYPE  342   20
     clus
vv    AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE
  NO                           140                            342
  YES                            9                             20
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 16(16P11.2) MUTATED                    115
  AMP PEAK 16(16P11.2) WILD-TYPE                  267
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(16P11.2) MUTATED                               7
  AMP PEAK 16(16P11.2) WILD-TYPE                            55
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 16(16P11.2) MUTATED                      47
  AMP PEAK 16(16P11.2) WILD-TYPE                    99
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 16(16P11.2) MUTATED                                0
  AMP PEAK 16(16P11.2) WILD-TYPE                             13
D16V10, multiclass
                                clus
vv                               AMP PEAK 16(16P11.2) MUTATED
  COLON ADENOCARCINOMA                                    115
  COLON MUCINOUS ADENOCARCINOMA                             7
  RECTAL ADENOCARCINOMA                                    47
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 16(16P11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      267
  COLON MUCINOUS ADENOCARCINOMA                              55
  RECTAL ADENOCARCINOMA                                      99
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(16P11.2) MUTATED   125   1  14   7
  AMP PEAK 16(16P11.2) WILD-TYPE 321   5  23  22
D16V11, multiclass
    clus
vv   AMP PEAK 16(16P11.2) MUTATED AMP PEAK 16(16P11.2) WILD-TYPE
  R0                          125                            321
  R1                            1                              5
  R2                           14                             23
  RX                            7                             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"
D16V12, continuous
D16V13, binary
                                cls
clus                               0   1
  AMP PEAK 16(16P11.2) MUTATED     2  98
  AMP PEAK 16(16P11.2) WILD-TYPE   3 254
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(16P11.2) MUTATED      2   98
  AMP PEAK 16(16P11.2) WILD-TYPE    3  254
                        clus
vv                       AMP PEAK 16(16P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           98
                        clus
vv                       AMP PEAK 16(16P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            254
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(17Q12) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(17Q12) MUTATED   129  24
  AMP PEAK 17(17Q12) WILD-TYPE 337 104
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                         153                          441 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                          24                          104 
$`AMP PEAK 17(17Q12) MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3556 
       24.33        14.53         1.02        58.03        36.03        23.01 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-A00L 
       36.00        85.05        24.03        12.99        50.99        38.04 
TCGA-AA-A00Z TCGA-AD-6888 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6314 TCGA-NH-A8F7 
       21.99        15.52         5.88        63.62        35.93        17.85 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       13.94        19.99        17.03        15.95        31.00        51.98 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE 
       55.76        26.43        15.62        12.66         1.61        39.45 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 
       43.76        43.43        37.02        36.53        30.44        29.19 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 
       32.71        29.16        27.09        25.08        25.18        24.69 
TCGA-A6-6782 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3532 
       20.28         1.02        37.05        38.99         0.00        29.00 
TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3679 TCGA-AA-3812 TCGA-AA-3821 TCGA-AA-3846 
       12.99        24.00        15.02        35.05         1.02        17.03 
TCGA-AA-3856 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3973 
        0.99        27.02        18.05        34.03         2.01        13.05 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A02O 
       27.02        27.02        32.02        12.00         1.02         0.92 
TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-A8YK 
       41.00        24.53        27.42        16.44        16.31        18.84 
TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-6715 
       88.21        12.10        29.56         3.19        12.69        12.59 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       14.30       148.01         8.02        13.02        29.06        22.03 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 
       17.03        14.04        29.03        21.99        14.99        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6532 TCGA-D5-6533 
       11.08        11.01        19.59        55.92        18.25        25.48 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A0XD 
       15.12         4.80        17.13        14.30        13.41        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A28M TCGA-F4-6704 TCGA-G4-6299 TCGA-G4-6303 
       38.20       130.65        95.18         1.55        74.56        65.85 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A6GB 
       55.04        39.42        36.00        26.43        46.75        15.65 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L 
       29.46        32.98        38.70        17.23        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 
       11.84        12.00         7.07        36.03        46.03        34.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3898 
       15.95        19.99         0.99        19.99         1.02        48.03 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A016 TCGA-AH-6643 TCGA-AH-6897 
       32.02        36.03         1.02         9.07        43.20        26.43 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 
        6.05        13.78        47.44        12.00        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 
       12.62        51.48        17.00        18.28        16.31        11.97 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 
       32.19        19.66        12.46 

$`AMP PEAK 17(17Q12) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       45.60        13.94        24.16        13.02        24.03        37.05 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 
        8.05        19.07        34.03         0.99        13.02        17.95 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 
       19.99        19.99         6.05         0.92        19.00        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       19.04        14.93        31.07        29.98        24.00         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       26.01        24.00        19.07        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       28.21        23.51        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A015 
       79.69        10.39         8.02        17.03        25.97        36.03 
TCGA-BM-6198 TCGA-G5-6233 TCGA-4N-A93T TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 
       21.24        18.28         4.80         9.53        43.76        46.65 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        34.65        32.75        32.45        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 
       33.53        23.61        22.09        22.06        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
        8.38        20.61        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        5.03         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3538 
        1.02         1.02         9.07        19.07        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       14.01        33.99        21.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       61.02        78.08         6.97        54.02         2.01        14.01 
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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 
        5.03        26.99        10.06         0.99        25.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 
       15.95        38.99        36.95        37.02         0.00        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 
        0.00        33.07         0.00        36.03        32.05        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       53.00        17.03        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
       26.01        20.98        21.99        16.08        34.06        25.02 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
        7.96        13.94        38.04        19.00        30.02        34.03 
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-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        10.98 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T 
       31.00        31.00        38.07         1.02        35.01        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        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-6889 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 
       12.16        83.24         5.79        22.42        26.47         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.92        14.50        27.09         0.95        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4308 
       21.44        17.82        17.26        17.85        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 
       65.00        62.79        49.41         6.77         5.23        11.74 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       10.06        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       20.02        37.02        25.02        26.04        27.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 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-6677 TCGA-CM-6679 TCGA-CM-6680 
       14.04        11.01        12.95        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       45.40        54.61        56.09        20.19        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       43.27        17.85        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D4 
       13.35        12.00        11.38        10.26       119.70        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB 
       49.91        13.32        12.59       140.38         7.50        44.32 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-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-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
        8.61        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       47.87        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 
        0.53        47.41        35.31       133.18         8.35        82.39 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 
       67.30        53.62        44.68        85.48        61.91        26.04 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 
        9.93        12.79        16.80        42.77         8.42        31.30 
TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 
       21.90        60.13        11.90        70.03        46.92        39.48 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 
       16.83        24.36        20.02        24.59        36.03        32.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 
       20.05        24.00         1.02        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3726 
       50.04        12.03         6.05         0.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
        0.99        29.98        37.02        32.98         0.99        19.04 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 
       25.02        19.99        28.04        14.04         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       20.98        13.94         6.02        23.01        37.02         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6620 
       38.04        38.56         2.50        27.55        19.46        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       44.78        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       26.04        31.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       44.02        25.97       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       20.91        15.85        17.69        16.34        16.41         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-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 
       49.51        42.35        28.57         0.39        36.49        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       38.14        11.87        47.08 

  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                           0                            0 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                      148.01                       140.38 
  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE 
                       23.01                        21.99 
[1] "0.0 - 148.0 (23.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.4"
D17V2, continuous
D17V3, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED   114  46
  AMP PEAK 17(17Q12) WILD-TYPE 334 116
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED    114   46
  AMP PEAK 17(17Q12) WILD-TYPE  334  116
        clus
vv       AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  COLON                         114                          334
  RECTUM                         46                          116
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 17(17Q12) MUTATED        22        0        8        42         1
  AMP PEAK 17(17Q12) WILD-TYPE      82        1       29       130        11
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 17(17Q12) MUTATED           1         4          4         21
  AMP PEAK 17(17Q12) WILD-TYPE         1        20         11         63
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 17(17Q12) MUTATED           18       25         8         1
  AMP PEAK 17(17Q12) WILD-TYPE         37       38        16         1
D17V4, multiclass
            clus
vv           AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  STAGE I                            22                           82
  STAGE IA                            0                            1
  STAGE II                            8                           29
  STAGE IIA                          42                          130
  STAGE IIB                           1                           11
  STAGE IIC                           1                            1
  STAGE III                           4                           20
  STAGE IIIA                          4                           11
  STAGE IIIB                         21                           63
  STAGE IIIC                         18                           37
  STAGE IV                           25                           38
  STAGE IVA                           8                           16
  STAGE IVB                           1                            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 17(17Q12) MUTATED     8  21 115  16
  AMP PEAK 17(17Q12) WILD-TYPE  12  84 302  53
D17V5, multiclass
    clus
vv   AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  T1                          8                           12
  T2                         21                           84
  T3                        115                          302
  T4                         16                           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 17(17Q12) MUTATED    83  39  38
  AMP PEAK 17(17Q12) WILD-TYPE 263 111  77
D17V6, multiclass
    clus
vv   AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  N0                         83                          263
  N1                         39                          111
  N2                         38                           77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED   103  34
  AMP PEAK 17(17Q12) WILD-TYPE 350  54
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED    103   34
  AMP PEAK 17(17Q12) WILD-TYPE  350   54
   clus
vv  AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  0                        103                          350
  1                         34                           54
[1] 2 2
[1] FALSE
D17V8, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED    66  94
  AMP PEAK 17(17Q12) WILD-TYPE 223 231
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED     66   94
  AMP PEAK 17(17Q12) WILD-TYPE  223  231
        clus
vv       AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  FEMALE                         66                          223
  MALE                           94                          231
[1] 2 2
[1] FALSE
D17V9, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED   125   7
  AMP PEAK 17(17Q12) WILD-TYPE 357  22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED    125    7
  AMP PEAK 17(17Q12) WILD-TYPE  357   22
     clus
vv    AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  NO                         125                          357
  YES                          7                           22
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 17(17Q12) MUTATED                    101
  AMP PEAK 17(17Q12) WILD-TYPE                  281
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(17Q12) MUTATED                              11
  AMP PEAK 17(17Q12) WILD-TYPE                            51
                              vv
clus                           RECTAL ADENOCARCINOMA
  AMP PEAK 17(17Q12) MUTATED                      44
  AMP PEAK 17(17Q12) WILD-TYPE                   102
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 17(17Q12) MUTATED                                2
  AMP PEAK 17(17Q12) WILD-TYPE                             11
D17V10, multiclass
                                clus
vv                               AMP PEAK 17(17Q12) MUTATED
  COLON ADENOCARCINOMA                                  101
  COLON MUCINOUS ADENOCARCINOMA                          11
  RECTAL ADENOCARCINOMA                                  44
  RECTAL MUCINOUS ADENOCARCINOMA                          2
                                clus
vv                               AMP PEAK 17(17Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    281
  COLON MUCINOUS ADENOCARCINOMA                            51
  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"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 17(17Q12) MUTATED   110   2  16   6
  AMP PEAK 17(17Q12) WILD-TYPE 336   4  21  23
D17V11, multiclass
    clus
vv   AMP PEAK 17(17Q12) MUTATED AMP PEAK 17(17Q12) WILD-TYPE
  R0                        110                          336
  R1                          2                            4
  R2                         16                           21
  RX                          6                           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"
D17V12, continuous
D17V13, binary
                              cls
clus                             0   1
  AMP PEAK 17(17Q12) MUTATED     3  90
  AMP PEAK 17(17Q12) WILD-TYPE   2 262
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17Q12) MUTATED      3   90
  AMP PEAK 17(17Q12) WILD-TYPE    2  262
                        clus
vv                       AMP PEAK 17(17Q12) MUTATED
  HISPANIC OR LATINO                              3
  NOT HISPANIC OR LATINO                         90
                        clus
vv                       AMP PEAK 17(17Q12) WILD-TYPE
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          262
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(17Q24.1) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 18(17Q24.1) MUTATED   121  19
  AMP PEAK 18(17Q24.1) WILD-TYPE 345 109
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                           140                            454 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                            19                            109 
$`AMP PEAK 18(17Q24.1) MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3556 TCGA-AA-3692 
       24.33        14.53         1.02        58.03        23.01        36.00 
TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-A00L 
       85.05        24.03        12.99        24.00        50.99        38.04 
TCGA-AA-A00Z TCGA-AD-6888 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 
       21.99        15.52         5.88        63.62        35.93        91.79 
TCGA-NH-A8F7 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       17.85        19.99        17.03        15.95        31.00        51.98 
TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE 
       55.76        15.62         4.80        12.66         1.61        39.45 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 
       43.43        42.28        37.02        36.53        30.44        29.19 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 
       32.71        29.16        27.09        25.08        25.18        24.69 
TCGA-A6-6782 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3553 TCGA-AA-3679 TCGA-AA-3812 
       20.28         1.02        37.05        24.00        15.02        35.05 
TCGA-AA-3821 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3956 
        1.02        17.03        10.06        36.03         0.99        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A004 
        2.01        21.99        13.05        34.06        27.02        13.94 
TCGA-AA-A01G TCGA-AA-A01S TCGA-AA-A01Z TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6963 
       12.00         1.02        37.02        41.00        24.53        27.42 
TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-CA-5254 
       16.44        14.50        16.31        88.21        29.56        12.69 
TCGA-CA-6715 TCGA-CK-4948 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       12.59       148.01         8.02        13.02        29.06        22.03 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6675 
       17.03        14.04        29.03        21.99        14.99        13.05 
TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6533 
       11.08        11.01        54.61        19.59        55.92        25.48 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6924 TCGA-D5-6929 TCGA-DM-A1D0 
       15.12         4.80        17.13        14.30        13.41       130.65 
TCGA-DM-A28M TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 
       95.18        74.56        65.85        55.04        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5YX TCGA-RU-A8FL 
       26.43        46.75        15.65        29.46        32.98        38.70 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 
       39.48        17.23        13.55        86.63        11.84        12.00 
TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3609 
        7.07        46.03        34.03        50.04        15.95        19.99 
TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A016 TCGA-AH-6643 TCGA-AH-6897 
       19.99        36.03         1.02         9.07        43.20        26.43 
TCGA-CI-6619 TCGA-CI-6621 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
        6.05        13.78        12.00        25.05        25.05       129.27 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 
       51.48         3.48         4.18        18.28        16.31        11.97 
TCGA-F5-6811 TCGA-F5-6864 
       32.19        12.46 

$`AMP PEAK 18(17Q24.1) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       45.60        13.94        24.16        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 
       36.03         8.05        19.07        34.03         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       17.95        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3952 
       19.04        19.04        14.93        31.07        29.98         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       26.01        24.00        19.07        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       28.21        23.51        22.09        35.80        26.17        79.69 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A015 
       10.39         8.02        13.94        17.03        25.97        36.03 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 
       21.24        18.28        26.43         9.53        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.76        42.90        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        34.65        32.75        32.45        32.91        31.63 
TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6140 
       33.53        23.61        22.09        22.06        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
        8.38        20.61        21.76        24.39        23.87        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       19.66        16.24        24.92        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        5.03         7.04         3.02        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        29.95        20.98        13.94        61.02        78.08 
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-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        11.01         5.98        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       10.06         0.99        25.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       36.95        37.02         0.00         0.00        33.07         0.00 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
       32.05        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       16.08        25.02         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        10.98        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-A029 
        1.02        35.01        33.04         1.02        26.01        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-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 
       39.98        18.05        40.96        12.16        83.24         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 
       22.42        26.47         0.46         0.92        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
       33.01         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       19.33        18.84       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
       32.94         5.13        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
        6.77        12.10         5.23        11.74         3.19        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.46        12.39        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 
       20.02        37.02        25.02        26.04        27.02        22.98 
TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       30.08        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-6161 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-6677 TCGA-CM-6679 TCGA-CM-6680 
       14.04        11.01        12.95        11.08        10.06        12.03 
TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       45.40        56.09        20.19        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
       43.27        17.85        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       12.39        10.13        12.43         9.04         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20        92.75        49.91        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-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-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
      133.18         8.35        82.39        67.30        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T 
       85.48        61.91        26.04        13.78        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       42.77         8.42        31.30        21.90        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       70.03        46.92        43.04        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       29.98        16.83        24.36        20.02        24.59        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       36.03        32.02        36.03        20.05        24.00         1.02 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03        34.03         2.01        12.03         6.05         0.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 
       32.02        19.99        28.04        14.04         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       20.98        13.94         6.02        23.01        37.02         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6620 
       38.04        38.56         2.50        27.55        19.46        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        44.02        25.97        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       57.24        24.13        32.61        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       17.00        15.85        17.69        16.34        16.41         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-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       49.51        42.35        28.57         0.39        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       37.18        38.14        11.87        47.08 

  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                          0.99                           0.00 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                        148.01                         140.38 
  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE 
                          24.0                           21.6 
[1] "1.0 - 148.0 (24.0)" "0.0 - 140.4 (21.6)"
[1] "hr=" "1.8"
D18V2, continuous
D18V3, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED   105  38
  AMP PEAK 18(17Q24.1) WILD-TYPE 343 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED    105   38
  AMP PEAK 18(17Q24.1) WILD-TYPE  343  124
        clus
vv       AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  COLON                           105                            343
  RECTUM                           38                            124
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 18(17Q24.1) MUTATED        21        0        5        42         2
  AMP PEAK 18(17Q24.1) WILD-TYPE      83        1       32       130        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(17Q24.1) MUTATED           1         4          3         22
  AMP PEAK 18(17Q24.1) WILD-TYPE         1        20         12         62
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 18(17Q24.1) MUTATED           12       19         7         1
  AMP PEAK 18(17Q24.1) WILD-TYPE         43       44        17         1
D18V4, multiclass
            clus
vv           AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  STAGE I                              21                             83
  STAGE IA                              0                              1
  STAGE II                              5                             32
  STAGE IIA                            42                            130
  STAGE IIB                             2                             10
  STAGE IIC                             1                              1
  STAGE III                             4                             20
  STAGE IIIA                            3                             12
  STAGE IIIB                           22                             62
  STAGE IIIC                           12                             43
  STAGE IV                             19                             44
  STAGE IVA                             7                             17
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 18(17Q24.1) MUTATED     4  23 104  13
  AMP PEAK 18(17Q24.1) WILD-TYPE  16  82 313  56
D18V5, multiclass
    clus
vv   AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  T1                            4                             16
  T2                           23                             82
  T3                          104                            313
  T4                           13                             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
  AMP PEAK 18(17Q24.1) MUTATED    80  37  27
  AMP PEAK 18(17Q24.1) WILD-TYPE 266 113  88
D18V6, multiclass
    clus
vv   AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  N0                           80                            266
  N1                           37                            113
  N2                           27                             88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED    96  27
  AMP PEAK 18(17Q24.1) WILD-TYPE 357  61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED     96   27
  AMP PEAK 18(17Q24.1) WILD-TYPE  357   61
   clus
vv  AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  0                           96                            357
  1                           27                             61
[1] 2 2
[1] FALSE
D18V8, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED    70  74
  AMP PEAK 18(17Q24.1) WILD-TYPE 219 251
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED     70   74
  AMP PEAK 18(17Q24.1) WILD-TYPE  219  251
        clus
vv       AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  FEMALE                           70                            219
  MALE                             74                            251
[1] 2 2
[1] FALSE
D18V9, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED   120   6
  AMP PEAK 18(17Q24.1) WILD-TYPE 362  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED    120    6
  AMP PEAK 18(17Q24.1) WILD-TYPE  362   23
     clus
vv    AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  NO                           120                            362
  YES                            6                             23
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 18(17Q24.1) MUTATED                     94
  AMP PEAK 18(17Q24.1) WILD-TYPE                  288
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(17Q24.1) MUTATED                              10
  AMP PEAK 18(17Q24.1) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 18(17Q24.1) MUTATED                      38
  AMP PEAK 18(17Q24.1) WILD-TYPE                   108
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 18(17Q24.1) MUTATED                                0
  AMP PEAK 18(17Q24.1) WILD-TYPE                             13
D18V10, multiclass
                                clus
vv                               AMP PEAK 18(17Q24.1) MUTATED
  COLON ADENOCARCINOMA                                     94
  COLON MUCINOUS ADENOCARCINOMA                            10
  RECTAL ADENOCARCINOMA                                    38
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 18(17Q24.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      288
  COLON MUCINOUS ADENOCARCINOMA                              52
  RECTAL ADENOCARCINOMA                                     108
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 18(17Q24.1) MUTATED   105   2  12   3
  AMP PEAK 18(17Q24.1) WILD-TYPE 341   4  25  26
D18V11, multiclass
    clus
vv   AMP PEAK 18(17Q24.1) MUTATED AMP PEAK 18(17Q24.1) WILD-TYPE
  R0                          105                            341
  R1                            2                              4
  R2                           12                             25
  RX                            3                             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"
D18V12, continuous
D18V13, binary
                                cls
clus                               0   1
  AMP PEAK 18(17Q24.1) MUTATED     3  86
  AMP PEAK 18(17Q24.1) WILD-TYPE   2 266
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17Q24.1) MUTATED      3   86
  AMP PEAK 18(17Q24.1) WILD-TYPE    2  266
                        clus
vv                       AMP PEAK 18(17Q24.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       AMP PEAK 18(17Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            266
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(19Q12) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 19(19Q12) MUTATED   106  24
  AMP PEAK 19(19Q12) WILD-TYPE 360 104
  AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE 
                         130                          464 
  AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE 
                          24                          104 
$`AMP PEAK 19(19Q12) MUTATED`
TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3506 TCGA-AA-3552 TCGA-AA-3939 TCGA-AA-3972 
       45.60        14.53        58.03        13.02        12.99        50.99 
TCGA-AA-A00Z TCGA-AD-6888 TCGA-G4-6310 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-A014 
       21.99        15.52        63.62        17.85        10.39        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE 
       36.03        31.00        21.24        15.62        12.66        39.45 
TCGA-A6-2671 TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 
       43.76        43.43        16.57        37.02        34.65        36.53 
TCGA-A6-5657 TCGA-A6-5667 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 
       31.63        29.16        25.08        25.18        21.76        23.87 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3502 TCGA-AA-3542 TCGA-AA-3685 TCGA-AA-3812 
       61.84        56.25        35.01        12.99        37.05        35.05 
TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3973 TCGA-AA-A00K 
        0.99        37.02        33.07        36.03        13.05        18.05 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01G TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
       27.02        42.02        12.00        51.98         2.96        39.98 
TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        0.92         5.79        22.42        26.47        16.44        14.50 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6606 
        0.20        17.85        18.84        88.21        29.56        11.74 
TCGA-CA-5255 TCGA-CA-6719 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4746 
       12.36        14.30        85.45        21.99         2.01        37.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6161 
       25.02        13.02        32.02         5.03        15.02        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6166 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6535 
       14.04        29.03        21.99        11.08        19.59        15.12 
TCGA-D5-6537 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0X9 
        4.80        11.64        13.41        12.00        11.38       119.70 
TCGA-DM-A28F TCGA-F4-6459 TCGA-F4-6855 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6311 
       35.97         8.61        47.41        82.39        74.56        39.42 
TCGA-G4-6320 TCGA-G4-6627 TCGA-QG-A5YW TCGA-QL-A97D TCGA-AF-2689 TCGA-AF-A56K 
       26.43        74.79        29.46        21.90        39.48        86.63 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3600 
       65.98        36.03        46.03        34.03        34.03         6.05 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4001 
       19.99        20.98         0.99        19.99         1.02        36.03 
TCGA-AG-4007 TCGA-AG-A016 TCGA-AG-A026 TCGA-AG-A032 TCGA-CI-6619 TCGA-CI-6621 
        1.02         9.07         1.94        38.04         6.05        13.78 
TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 
       48.20        21.01        25.05        12.00        51.98        25.05 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 
      129.27        24.13         3.48        20.55        17.69        16.31 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6863 
       11.51        13.64        11.97        11.87 

$`AMP PEAK 19(19Q12) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        13.94        24.16         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 
       31.07        24.03        29.98        24.00         2.01        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       24.00        19.07        38.04        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       26.17        91.79        79.69         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       17.03        17.03        25.97        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
       26.43         4.80         1.61         9.53        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        44.91        35.11        37.05        37.25 
TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 
       32.75        32.45        32.91        30.44        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       23.61        22.09        22.06        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       24.13         8.38        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A5ZU TCGA-AA-3488 
       19.66        20.28        16.24        24.92         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02         1.02        37.05        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        26.01        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
       10.06        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 
       36.95         0.00        17.03        10.06         0.00         0.00 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 
       20.98        34.03         2.01        21.99        16.08        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00R 
       19.00        30.02        34.03        18.05         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        10.98 
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-A02H 
        1.02        33.04         1.02        26.01        37.02         2.01 
TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03        22.03        41.00        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 
       12.16        83.24        24.53        27.42         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.26        19.33       109.28        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
       32.94         5.13        22.36        65.00        62.79        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 
        6.77        12.10         5.23         3.19        12.69        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       17.56       148.01        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4748 TCGA-CM-4750 
       82.95       124.27        23.05        20.02        26.04         8.02 
TCGA-CM-4751 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 
       27.02        29.06        22.03        22.98        30.08        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6167 TCGA-CM-6168 
       15.02        17.03        12.00        16.04        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-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       56.09        55.92        20.19        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       25.48        43.27        17.85        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-D5-6930 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF 
        9.04         9.44        13.35        10.26        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
      130.65        92.75        49.91        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        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        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
        6.18        47.87         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       33.67        13.25         0.53        35.31       133.18         8.35 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A50T 
       61.91        36.00        26.04        13.78        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       16.80        42.77        32.98         8.42        31.30        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       60.13        11.90        70.03        46.92        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.36        20.02        24.59        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 
       32.02         7.07        20.05        24.00         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-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        0.99        29.98        37.02        32.98         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        28.04        14.04 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       37.02         1.02         1.02        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        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       19.46        33.17        44.78        47.44        78.12         7.17 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       26.04        31.00        13.97        31.00        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        12.62       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         4.18        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        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE 
                         0.2                          0.0 
  AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE 
                      129.27                       148.01 
  AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE 
                      21.945                       22.075 
[1] "0.2 - 129.3 (21.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.2"
D19V2, continuous
D19V3, binary
                              cls
clus                             0   1
  AMP PEAK 19(19Q12) MUTATED    95  44
  AMP PEAK 19(19Q12) WILD-TYPE 353 118
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(19Q12) MUTATED     95   44
  AMP PEAK 19(19Q12) WILD-TYPE  353  118
        clus
vv       AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE
  COLON                          95                          353
  RECTUM                         44                          118
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 19(19Q12) MUTATED        22        0        5        36         1
  AMP PEAK 19(19Q12) WILD-TYPE      82        1       32       136        11
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(19Q12) MUTATED           1         4          2         23
  AMP PEAK 19(19Q12) WILD-TYPE         1        20         13         61
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 19(19Q12) MUTATED           14       22         6         0
  AMP PEAK 19(19Q12) WILD-TYPE         41       41        18         2
D19V4, multiclass
            clus
vv           AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE
  STAGE I                            22                           82
  STAGE IA                            0                            1
  STAGE II                            5                           32
  STAGE IIA                          36                          136
  STAGE IIB                           1                           11
  STAGE IIC                           1                            1
  STAGE III                           4                           20
  STAGE IIIA                          2                           13
  STAGE IIIB                         23                           61
  STAGE IIIC                         14                           41
  STAGE IV                           22                           41
  STAGE IVA                           6                           18
  STAGE IVB                           0                            2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 19(19Q12) MUTATED     3  22  98  16
  AMP PEAK 19(19Q12) WILD-TYPE  17  83 319  53
D19V5, multiclass
    clus
vv   AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE
  T1                          3                           17
  T2                         22                           83
  T3                         98                          319
  T4                         16                           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 19(19Q12) MUTATED    69  43  27
  AMP PEAK 19(19Q12) WILD-TYPE 277 107  88
D19V6, multiclass
    clus
vv   AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE
  N0                         69                          277
  N1                         43                          107
  N2                         27                           88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                              cls
clus                             0   1
  AMP PEAK 19(19Q12) MUTATED    91  28
  AMP PEAK 19(19Q12) WILD-TYPE 362  60
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(19Q12) MUTATED     91   28
  AMP PEAK 19(19Q12) WILD-TYPE  362   60
   clus
vv  AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE
  0                         91                          362
  1                         28                           60
[1] 2 2
[1] FALSE
D19V8, binary
                              cls
clus                             0   1
  AMP PEAK 19(19Q12) MUTATED    59  80
  AMP PEAK 19(19Q12) WILD-TYPE 230 245
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(19Q12) MUTATED     59   80
  AMP PEAK 19(19Q12) WILD-TYPE  230  245
        clus
vv       AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE
  FEMALE                         59                          230
  MALE                           80                          245
[1] 2 2
[1] FALSE
D19V9, binary
                              cls
clus                             0   1
  AMP PEAK 19(19Q12) MUTATED   106   7
  AMP PEAK 19(19Q12) WILD-TYPE 376  22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(19Q12) MUTATED    106    7
  AMP PEAK 19(19Q12) WILD-TYPE  376   22
     clus
vv    AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE
  NO                         106                          376
  YES                          7                           22
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 19(19Q12) MUTATED                     84
  AMP PEAK 19(19Q12) WILD-TYPE                  298
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(19Q12) MUTATED                              11
  AMP PEAK 19(19Q12) WILD-TYPE                            51
                              vv
clus                           RECTAL ADENOCARCINOMA
  AMP PEAK 19(19Q12) MUTATED                      44
  AMP PEAK 19(19Q12) WILD-TYPE                   102
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 19(19Q12) MUTATED                                0
  AMP PEAK 19(19Q12) WILD-TYPE                             13
D19V10, multiclass
                                clus
vv                               AMP PEAK 19(19Q12) MUTATED
  COLON ADENOCARCINOMA                                   84
  COLON MUCINOUS ADENOCARCINOMA                          11
  RECTAL ADENOCARCINOMA                                  44
  RECTAL MUCINOUS ADENOCARCINOMA                          0
                                clus
vv                               AMP PEAK 19(19Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                    298
  COLON MUCINOUS ADENOCARCINOMA                            51
  RECTAL ADENOCARCINOMA                                   102
  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"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 19(19Q12) MUTATED    98   3  11   7
  AMP PEAK 19(19Q12) WILD-TYPE 348   3  26  22
D19V11, multiclass
    clus
vv   AMP PEAK 19(19Q12) MUTATED AMP PEAK 19(19Q12) WILD-TYPE
  R0                         98                          348
  R1                          3                            3
  R2                         11                           26
  RX                          7                           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"
D19V12, continuous
D19V13, binary
                              cls
clus                             0   1
  AMP PEAK 19(19Q12) MUTATED     2  85
  AMP PEAK 19(19Q12) WILD-TYPE   3 267
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 19(19Q12) MUTATED      2   85
  AMP PEAK 19(19Q12) WILD-TYPE    3  267
                        clus
vv                       AMP PEAK 19(19Q12) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         85
                        clus
vv                       AMP PEAK 19(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          267
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(20P12.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(20P12.1) MUTATED   214  56
  AMP PEAK 20(20P12.1) WILD-TYPE 252  72
  AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE 
                           270                            324 
  AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE 
                            56                             72 
$`AMP PEAK 20(20P12.1) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3520 TCGA-AA-3530 
       45.60        13.94        24.16        58.03        24.03        19.07 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       13.02        23.01        19.99         6.05        19.00        36.00 
TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       14.93        12.99        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6895 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 
       38.04        21.99        25.08       106.75        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 
       28.21        63.62        35.93        91.79        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B 
       36.03        51.98        21.24        18.28        55.76        15.62 
TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 
        4.80        39.45        43.76        43.76        43.43        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       35.11        16.57        37.02        34.65        36.53        32.45 
TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-6137 TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6782 
       32.91        30.44        27.09        25.08        24.69        20.28 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 
       61.84         9.63         5.03         7.04         1.02         6.97 
TCGA-AA-3514 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3549 
        1.02         0.00        29.00        29.00        14.01        21.01 
TCGA-AA-3558 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 
       20.98         2.01        14.01        50.04        47.05        15.02 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3842 TCGA-AA-3845 
       37.05         5.03        10.06         0.99        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03        10.06        33.07         0.99        31.07        17.03 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 
       18.05        24.00        34.03        21.99        13.05        34.06 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U 
       27.02         7.96        13.94        18.05         4.01        17.03 
TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
       14.99        15.02        10.98        12.00        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       26.01        51.98         2.96         2.01         5.03         0.92 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       41.00        39.98        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A54L TCGA-AY-A69D 
       27.42        16.44        16.31         0.95        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6598 
       19.33        18.84         1.41         5.13        65.00        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       12.10        29.56         3.19        12.69        12.36        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CM-4744 
       12.59        12.59        14.30        17.56        85.45        20.02 
TCGA-CM-4747 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5862 TCGA-CM-5863 
       25.02        13.02        29.06        22.98         5.03        15.02 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       15.02        17.03        15.02        14.04        16.04        21.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-5538 
       14.04        11.01        11.08        11.01        45.40        54.61 
TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6539 TCGA-D5-6920 TCGA-D5-6922 
       19.59        20.19        17.75        12.49        12.39        10.13 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D8 
        9.04        11.64        13.41        10.26       119.70        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28H 
        7.50        44.32       139.17        14.04        35.97       117.07 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6855 
       95.18         8.61        35.74         6.18         1.55        47.41 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6322 
      133.18        82.39        55.04        39.42        36.00        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC 
       13.78        46.75        74.79        18.18        15.65        12.79 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2693 
       42.77        29.46        32.98        46.92        17.23        37.97 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3582 
       37.74        29.98        16.83        20.02        24.59        36.03 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3878 
        0.99        19.99        20.98        29.98        37.02         0.99 
TCGA-AG-3887 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-4005 
       36.95        14.01        48.03        25.02        19.99        14.04 
TCGA-AG-4007 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A02X 
        1.02         6.02        23.01        37.02         9.07        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04        38.56        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-DC-4745 TCGA-DC-4749 
        6.05        13.78        44.78        47.44        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
       26.04        31.00        13.97        31.00        51.98        25.97 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
      126.44       129.27        20.55        20.91        17.00        18.28 
TCGA-EI-6514 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
       16.31        13.64        11.97         9.96        49.51         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       32.19        36.49        37.18        38.14        11.87        47.08 

$`AMP PEAK 20(20P12.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 
       24.33        14.53         1.02        13.02        37.05        36.03 
TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 
        8.05        34.03         0.99        17.95        19.99         0.92 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       85.05        19.04        19.04        31.07        24.03        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6964 
       24.00         2.01        39.06        21.37        15.52        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6298 TCGA-G4-6321 TCGA-G4-6586 
       75.95       100.01         1.94        23.51        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A014 TCGA-AG-A01N TCGA-G5-6641 TCGA-4T-AA8H 
       26.17        79.69        15.95        31.00        26.43        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 
        1.61         9.53        46.65        42.90        42.28        37.05 
TCGA-A6-2685 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       37.25        32.75        31.63        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 
       22.09        22.06        32.71        29.16        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
        8.38        25.18        20.61        21.76        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3492 
       20.12        19.66        16.24        24.92        56.25         3.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       37.05        35.01        63.98        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 
       19.07        26.01        12.99        33.99        24.00        29.95 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3678 
       13.94        61.02        78.08         6.97        54.02        47.01 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 
       11.01         5.98        26.99        35.05        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3852 
       17.98        15.95        38.99        36.95         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 
       36.03        32.05        53.00        27.02        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3977 
       33.01        26.01        20.98         2.01        16.08        25.02 
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-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F 
       27.02        42.02         0.99        34.98        15.02        32.02 
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         1.02 
TCGA-AA-A01Z TCGA-AA-A02F TCGA-AA-A02R TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-6889 
       37.02        39.98        22.03        18.05        40.96        83.24 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-5543 
       26.47         0.46         0.92        14.50        27.09        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 
        0.20        21.44        17.82       109.28        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6605 
       32.94        22.36        62.79        88.21         6.77         5.23 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 
       11.74        12.39        12.20        12.76        10.06       148.01 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
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-5344 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6162 
       27.02        22.03        30.08        32.02        15.02        12.00 
TCGA-CM-6164 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6674 
       29.03        14.99        12.99        13.02        15.02        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-5541 
       13.05        11.08        10.06        12.03        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6923 
        4.80        17.13        16.14        15.58         7.53        12.43 
TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XD 
       14.30         9.44        13.35        12.00        11.38        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E 
      131.51       135.65         7.76        26.47        81.37       119.93 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 
       60.79        98.24        31.96        11.11        35.74        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31         8.35        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6315 TCGA-G4-6320 TCGA-NH-A50U TCGA-NH-A50V 
       44.68        85.48        61.91        26.43        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       19.33         9.93        16.80         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 
       38.70        60.13        11.90        70.03        39.48        43.04 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       13.55        34.49        24.36        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00        32.02         7.07        20.05        24.00 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 
       34.03         2.01         6.05        15.95         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 
       13.02        35.01         1.02        32.02        28.04        36.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A020 
        3.98        46.03        20.98        13.94         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-CI-6620 
       49.97         1.94        38.96        61.97         2.50        33.17 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 
       48.20        78.12         7.17        12.00        10.98        44.02 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        25.05        12.62        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6511 
       51.48        32.61         3.48         4.18        19.96        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-6917 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 
       17.46         8.45        42.35        28.57        19.66        12.46 

  AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE 
                             0                              0 
  AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE 
                        139.17                         148.01 
  AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE 
                        20.415                         23.740 
[1] "0.0 - 139.2 (20.4)" "0.0 - 148.0 (23.7)"
[1] "hr=" "1"  
D20V2, continuous
D20V3, binary
                                cls
clus                               0   1
  AMP PEAK 20(20P12.1) MUTATED   194  81
  AMP PEAK 20(20P12.1) WILD-TYPE 254  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(20P12.1) MUTATED    194   81
  AMP PEAK 20(20P12.1) WILD-TYPE  254   81
        clus
vv       AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE
  COLON                           194                            254
  RECTUM                           81                             81
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 20(20P12.1) MUTATED        50        1       10        69         4
  AMP PEAK 20(20P12.1) WILD-TYPE      54        0       27       103         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(20P12.1) MUTATED           0         9          8         35
  AMP PEAK 20(20P12.1) WILD-TYPE         2        15          7         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 20(20P12.1) MUTATED           24       42        12         1
  AMP PEAK 20(20P12.1) WILD-TYPE         31       21        12         1
D20V4, multiclass
            clus
vv           AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE
  STAGE I                              50                             54
  STAGE IA                              1                              0
  STAGE II                             10                             27
  STAGE IIA                            69                            103
  STAGE IIB                             4                              8
  STAGE IIC                             0                              2
  STAGE III                             9                             15
  STAGE IIIA                            8                              7
  STAGE IIIB                           35                             49
  STAGE IIIC                           24                             31
  STAGE IV                             42                             21
  STAGE IVA                            12                             12
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 20(20P12.1) MUTATED     9  51 185  30
  AMP PEAK 20(20P12.1) WILD-TYPE  11  54 232  39
D20V5, multiclass
    clus
vv   AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE
  T1                            9                             11
  T2                           51                             54
  T3                          185                            232
  T4                           30                             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
  AMP PEAK 20(20P12.1) MUTATED   142  75  58
  AMP PEAK 20(20P12.1) WILD-TYPE 204  75  57
D20V6, multiclass
    clus
vv   AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE
  N0                          142                            204
  N1                           75                             75
  N2                           58                             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  AMP PEAK 20(20P12.1) MUTATED   186  54
  AMP PEAK 20(20P12.1) WILD-TYPE 267  34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(20P12.1) MUTATED    186   54
  AMP PEAK 20(20P12.1) WILD-TYPE  267   34
   clus
vv  AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE
  0                          186                            267
  1                           54                             34
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(20P12.1) MUTATED   117 161
  AMP PEAK 20(20P12.1) WILD-TYPE 172 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(20P12.1) MUTATED    117  161
  AMP PEAK 20(20P12.1) WILD-TYPE  172  164
        clus
vv       AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE
  FEMALE                          117                            172
  MALE                            161                            164
[1] 2 2
[1] FALSE
D20V9, binary
                                cls
clus                               0   1
  AMP PEAK 20(20P12.1) MUTATED   218  18
  AMP PEAK 20(20P12.1) WILD-TYPE 264  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(20P12.1) MUTATED    218   18
  AMP PEAK 20(20P12.1) WILD-TYPE  264   11
     clus
vv    AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE
  NO                           218                            264
  YES                           18                             11
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  AMP PEAK 20(20P12.1) MUTATED                    174
  AMP PEAK 20(20P12.1) WILD-TYPE                  208
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(20P12.1) MUTATED                              19
  AMP PEAK 20(20P12.1) WILD-TYPE                            43
                                vv
clus                             RECTAL ADENOCARCINOMA
  AMP PEAK 20(20P12.1) MUTATED                      76
  AMP PEAK 20(20P12.1) WILD-TYPE                    70
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 20(20P12.1) MUTATED                                3
  AMP PEAK 20(20P12.1) WILD-TYPE                             10
D20V10, multiclass
                                clus
vv                               AMP PEAK 20(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                    174
  COLON MUCINOUS ADENOCARCINOMA                            19
  RECTAL ADENOCARCINOMA                                    76
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK 20(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      208
  COLON MUCINOUS ADENOCARCINOMA                              43
  RECTAL ADENOCARCINOMA                                      70
  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"
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 20(20P12.1) MUTATED   199   3  23  10
  AMP PEAK 20(20P12.1) WILD-TYPE 247   3  14  19
D20V11, multiclass
    clus
vv   AMP PEAK 20(20P12.1) MUTATED AMP PEAK 20(20P12.1) WILD-TYPE
  R0                          199                            247
  R1                            3                              3
  R2                           23                             14
  RX                           10                             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"
D20V12, continuous
D20V13, binary
                                cls
clus                               0   1
  AMP PEAK 20(20P12.1) MUTATED     2 155
  AMP PEAK 20(20P12.1) WILD-TYPE   3 197
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(20P12.1) MUTATED      2  155
  AMP PEAK 20(20P12.1) WILD-TYPE    3  197
                        clus
vv                       AMP PEAK 20(20P12.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          155
                        clus
vv                       AMP PEAK 20(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            197
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(20P11.21) MUTATION ANALYSIS
D21V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 21(20P11.21) MUTATED   277  73
  AMP PEAK 21(20P11.21) WILD-TYPE 189  55
  AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE 
                            350                             244 
  AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE 
                             73                              55 
$`AMP PEAK 21(20P11.21) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3530 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 
       58.03        19.07        13.02        23.01        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3972 
       19.00        36.00        85.05        14.93        12.99        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 
       26.01        24.00        19.07        38.04        21.99        21.37 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       25.08       106.75         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 
       23.51        63.62        35.93        91.79        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       26.43        15.62         4.80         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2686 
       43.76        43.43        44.91        35.11        16.57        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       34.65        36.53        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-A6-6652 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.69        20.28        61.84         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3532 
        1.02         6.97         1.02        38.99         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3558 TCGA-AA-3660 
       29.00        12.99        14.01        21.01        20.98        78.08 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3685 
        2.01        14.01        50.04        47.05        15.02        37.05 
TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3842 
        5.03        10.06         0.99        25.02        38.99        37.02 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
        0.00        17.03        10.06        33.07         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       17.03        27.02        18.05        24.00        20.98        34.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
        2.01        21.99        16.08        13.05        34.06        27.02 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00U TCGA-AA-A00W 
        7.96        13.94        18.05         4.01        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01T 
       15.02        15.02        10.98        12.00        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 
        0.92        41.00        39.98        40.96        12.16        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
        5.79        22.42        27.42        26.47        16.44        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       16.31         0.95         0.20        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6598 
       18.84         1.41         5.13        65.00        62.79        49.41 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       12.10        29.56         3.19        12.69        12.36        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 
       12.59        12.59        12.20        14.30        17.56        85.45 
TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       21.99        20.02        25.02         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        14.04        29.03        16.04        21.99 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 
       13.02        15.02        14.04        11.01        11.08        11.01 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 
       10.06        45.40        54.61        19.59        55.92        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6898 
       17.75        18.25        25.48        43.27        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-A288 TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
      139.17        14.04       119.93        35.97       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6808 
        8.61        31.96        35.74         6.18         1.55        33.67 
TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 
       13.25        47.41       133.18         8.35        82.39        65.85 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6323 
       44.68        55.04        39.42        61.91        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV 
       46.75        74.79        18.18        15.65        12.79        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-T9-A92H TCGA-AF-2687 
       29.46        32.98         8.42        21.90        11.90        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 
       39.48        17.23        37.97        37.74        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 
       24.59        86.63        11.84        36.03         7.07        36.03 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03        34.03        50.04        12.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 
       15.95        19.99        20.98         7.99        29.98        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3894 
        0.99         0.99        19.99         1.02        36.95        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 
        1.02        48.03        25.02        32.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       14.04         1.02         6.02        23.01        37.02         9.07 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04        38.56        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
       19.46         6.05        13.78        44.78        47.44        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA 
       13.97        31.00        51.98        25.97        25.05       126.44 
TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6508 
       41.36       129.27        51.48         3.48        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
       17.00        18.28        17.69        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       13.64        11.97         9.96        49.51        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

$`AMP PEAK 21(20P11.21) WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3531 
       13.02        24.03        37.05        36.03         8.05        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 
        0.99        17.95        19.99         0.92        19.04        19.04 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-A024 
       31.07        24.03        29.98        24.00         2.01        39.06 
TCGA-AD-6888 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 
       15.52        10.88        75.95       100.01        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-A01N TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 
       26.17        79.69        31.00        12.66         9.53        46.65 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3809 TCGA-A6-5657 
       42.90        42.28        37.05        37.25        32.75        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        56.25         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3548 
       63.98         1.02         9.07        19.07        26.01        33.99 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 
       24.00        29.95        13.94        61.02         6.97        54.02 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3821 
       47.01        11.01         5.98        26.99        35.05         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
       17.98        15.95        36.95         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       32.05        53.00        31.00         2.01        33.01        26.01 
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-A01F 
       18.05        27.02        42.02         0.99        34.98        32.02 
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         1.02 
TCGA-AA-A01Z TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 TCGA-AM-5820 TCGA-AM-5821 
       37.02        22.03        18.05        83.24         0.46         0.92 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4308 TCGA-AZ-4315 
       27.09        33.01        21.44        17.82       109.28        58.39 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6605 
        5.65        32.94        22.36        88.21         6.77         5.23 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4948 TCGA-CK-4951 
       11.74        12.39        12.76        10.06       148.01        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5349 TCGA-CM-5861 
       23.05        37.02        26.04        27.02        30.08        15.02 
TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       12.00        14.99        12.99        12.95        13.05        11.08 
TCGA-CM-6680 TCGA-D5-5540 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       12.03        56.09        20.42        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       17.13        16.14        15.58        12.43        14.30         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       13.35        12.00        11.38        38.20        92.75        49.91 
TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28A 
       13.32       140.38        44.32       135.65         7.76        26.47 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6703 
       81.37        60.79        98.24        11.11        35.74        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6299 
       34.42        41.42        43.04         0.53        35.31        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50U 
       67.30        53.62        85.48        36.00        26.43        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       19.33        19.33         9.93        16.80        31.30        38.70 
TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 
       60.13        70.03        43.04        13.55        34.49        29.98 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3584 
       24.36        65.98        12.00        32.02        20.05        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-3881 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4021 
       19.04        17.95        13.02        35.01        28.04         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       46.03        20.98        13.94         1.02         1.02        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         2.50        33.17        48.20 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF 
       10.98        44.02        25.05        12.62        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
       32.61         4.18        19.96        15.85        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6571 
        8.61        17.46         8.45        42.35 

  AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE 
                              0                               0 
  AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE 
                         139.17                          148.01 
  AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE 
                          20.98                           24.00 
[1] "0.0 - 139.2 (21.0)" "0.0 - 148.0 (24.0)"
[1] "hr=" "1"  
D21V2, continuous
D21V3, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20P11.21) MUTATED   250 110
  AMP PEAK 21(20P11.21) WILD-TYPE 198  52
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20P11.21) MUTATED    250  110
  AMP PEAK 21(20P11.21) WILD-TYPE  198   52
        clus
vv       AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE
  COLON                            250                             198
  RECTUM                           110                              52
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 21(20P11.21) MUTATED        64        1       17        96         5
  AMP PEAK 21(20P11.21) WILD-TYPE      40        0       20        76         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(20P11.21) MUTATED           1         9         12         46
  AMP PEAK 21(20P11.21) WILD-TYPE         1        15          3         38
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 21(20P11.21) MUTATED           31       48        16         1
  AMP PEAK 21(20P11.21) WILD-TYPE         24       15         8         1
D21V4, multiclass
            clus
vv           AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE
  STAGE I                               64                              40
  STAGE IA                               1                               0
  STAGE II                              17                              20
  STAGE IIA                             96                              76
  STAGE IIB                              5                               7
  STAGE IIC                              1                               1
  STAGE III                              9                              15
  STAGE IIIA                            12                               3
  STAGE IIIB                            46                              38
  STAGE IIIC                            31                              24
  STAGE IV                              48                              15
  STAGE IVA                             16                               8
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 21(20P11.21) MUTATED    13  66 243  37
  AMP PEAK 21(20P11.21) WILD-TYPE   7  39 174  32
D21V5, multiclass
    clus
vv   AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE
  T1                            13                               7
  T2                            66                              39
  T3                           243                             174
  T4                            37                              32
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 21(20P11.21) MUTATED   196  95  68
  AMP PEAK 21(20P11.21) WILD-TYPE 150  55  47
D21V6, multiclass
    clus
vv   AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE
  N0                           196                             150
  N1                            95                              55
  N2                            68                              47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20P11.21) MUTATED   251  65
  AMP PEAK 21(20P11.21) WILD-TYPE 202  23
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20P11.21) MUTATED    251   65
  AMP PEAK 21(20P11.21) WILD-TYPE  202   23
   clus
vv  AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE
  0                           251                             202
  1                            65                              23
[1] 2 2
[1] FALSE
D21V8, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20P11.21) MUTATED   158 204
  AMP PEAK 21(20P11.21) WILD-TYPE 131 121
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20P11.21) MUTATED    158  204
  AMP PEAK 21(20P11.21) WILD-TYPE  131  121
        clus
vv       AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE
  FEMALE                           158                             131
  MALE                             204                             121
[1] 2 2
[1] FALSE
D21V9, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20P11.21) MUTATED   285  20
  AMP PEAK 21(20P11.21) WILD-TYPE 197   9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20P11.21) MUTATED    285   20
  AMP PEAK 21(20P11.21) WILD-TYPE  197    9
     clus
vv    AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE
  NO                            285                             197
  YES                            20                               9
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 21(20P11.21) MUTATED                    226
  AMP PEAK 21(20P11.21) WILD-TYPE                  156
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(20P11.21) MUTATED                              23
  AMP PEAK 21(20P11.21) WILD-TYPE                            39
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 21(20P11.21) MUTATED                     105
  AMP PEAK 21(20P11.21) WILD-TYPE                    41
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 21(20P11.21) MUTATED                                4
  AMP PEAK 21(20P11.21) WILD-TYPE                              9
D21V10, multiclass
                                clus
vv                               AMP PEAK 21(20P11.21) MUTATED
  COLON ADENOCARCINOMA                                     226
  COLON MUCINOUS ADENOCARCINOMA                             23
  RECTAL ADENOCARCINOMA                                    105
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               AMP PEAK 21(20P11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                       156
  COLON MUCINOUS ADENOCARCINOMA                               39
  RECTAL ADENOCARCINOMA                                       41
  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"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 21(20P11.21) MUTATED   261   4  25  14
  AMP PEAK 21(20P11.21) WILD-TYPE 185   2  12  15
D21V11, multiclass
    clus
vv   AMP PEAK 21(20P11.21) MUTATED AMP PEAK 21(20P11.21) WILD-TYPE
  R0                           261                             185
  R1                             4                               2
  R2                            25                              12
  RX                            14                              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"
D21V12, continuous
D21V13, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20P11.21) MUTATED     4 209
  AMP PEAK 21(20P11.21) WILD-TYPE   1 143
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20P11.21) MUTATED      4  209
  AMP PEAK 21(20P11.21) WILD-TYPE    1  143
                        clus
vv                       AMP PEAK 21(20P11.21) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           209
                        clus
vv                       AMP PEAK 21(20P11.21) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             143
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(20Q11.21) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 22(20Q11.21) MUTATED   357  94
  AMP PEAK 22(20Q11.21) WILD-TYPE 109  34
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                            451                             143 
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                             94                              34 
$`AMP PEAK 22(20Q11.21) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       14.93        31.07        24.03        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       25.08       106.75         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 
       23.51        63.62        35.93        91.79        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE 
       55.76        26.43        15.62         4.80         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.76        43.43        44.91        35.11        16.57 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        34.65        36.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       22.52        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        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3514 
        5.03         7.04         1.02        37.05         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       20.98        13.94        78.08         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.05        47.01        15.02         5.98        37.05         5.03 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       10.06        35.05         0.99        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       37.02         0.00        17.03        10.06        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 
        0.99        31.07        17.03        27.02        18.05        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-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       34.06        27.02         7.96        13.94        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       31.00         1.02        33.04        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        2.96        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       27.42        26.47        16.44         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
        0.95        33.01         0.20        17.26        17.85        19.33 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       18.84       109.28         1.41         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       62.79        49.41        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
       12.69        12.36        12.46        12.59        12.59        12.20 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 
       14.30        17.56       148.01        85.45        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        25.02         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        32.02         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        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 
       54.61        19.59        56.09        55.92        20.19        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
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-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M 
       14.04        26.47       119.93        35.97       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 
        8.61        31.96        35.74        35.74         6.18         1.55 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 
      133.18         8.35        82.39        65.85        44.68        55.04 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       39.42        61.91        36.00        26.43        26.04        13.78 
TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC 
       46.75        74.79        18.18        19.33        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       16.80        42.77        29.46        32.98         8.42        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       38.70        60.13        11.90        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       43.04        37.97        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       34.03        34.03        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       37.02         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       36.95        35.01        14.01         1.02        48.03        25.02 
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-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02         1.02         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        6.05        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        25.05       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         3.48         4.18        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-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

$`AMP PEAK 22(20Q11.21) WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
        0.92        19.04        19.04        29.98        24.00         2.01 
TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 
       39.06        10.88        75.95       100.01        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       26.17        79.69        12.66         9.53        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 
       42.28        37.05        32.75        31.63        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       22.06         8.38        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 
       24.92         3.02        35.01        63.98         1.02        29.95 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3710 TCGA-AA-3821 
       61.02         6.97        54.02        11.01        26.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 
       17.98        15.95         0.00         0.00        36.03        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-3994 
       31.00         2.01        33.01        26.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P 
       38.04        30.02        18.05         0.99        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 
        1.02        35.01         1.02        22.03        18.05        83.24 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AZ-4315 TCGA-AZ-4614 
        0.92        27.09        21.44        17.82        58.39         5.65 
TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 
       32.94        88.21         6.77        11.74        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       10.06        70.16        15.62        51.32        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 
      124.27        23.05        26.04        27.02        15.02        12.00 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 
       12.95        13.05        12.03        20.42        16.14        15.58 
TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 
        9.44        13.35        12.00       140.38       135.65         7.76 
TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6805 
       81.37        60.79        98.24        11.11        47.87        34.42 
TCGA-F4-6856 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-NH-A50U 
       35.31        74.56        67.30        53.62        85.48        10.98 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3400 
       19.33         9.93        31.30        70.03        13.55        34.49 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 
       12.00        32.02         2.01         6.05        32.98        19.04 
TCGA-AG-3892 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-CI-6620 
       13.02         3.98        20.98        49.97        61.97        33.17 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       12.62        19.96         8.61        17.46         8.45 

  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                              0                               0 
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE 
                          21.99                           22.06 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (22.1)"
[1] "hr=" "1"  
D22V2, continuous
D22V3, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q11.21) MUTATED   320 144
  AMP PEAK 22(20Q11.21) WILD-TYPE 128  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED    320  144
  AMP PEAK 22(20Q11.21) WILD-TYPE  128   18
        clus
vv       AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  COLON                            320                             128
  RECTUM                           144                              18
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 22(20Q11.21) MUTATED        79        1       22       118         6
  AMP PEAK 22(20Q11.21) WILD-TYPE      25        0       15        54         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(20Q11.21) MUTATED           2        18         14         68
  AMP PEAK 22(20Q11.21) WILD-TYPE         0         6          1         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 22(20Q11.21) MUTATED           45       56        21         1
  AMP PEAK 22(20Q11.21) WILD-TYPE         10        7         3         1
D22V4, multiclass
            clus
vv           AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  STAGE I                               79                              25
  STAGE IA                               1                               0
  STAGE II                              22                              15
  STAGE IIA                            118                              54
  STAGE IIB                              6                               6
  STAGE IIC                              2                               0
  STAGE III                             18                               6
  STAGE IIIA                            14                               1
  STAGE IIIB                            68                              16
  STAGE IIIC                            45                              10
  STAGE IV                              56                               7
  STAGE IVA                             21                               3
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 22(20Q11.21) MUTATED    14  84 320  46
  AMP PEAK 22(20Q11.21) WILD-TYPE   6  21  97  23
D22V5, multiclass
    clus
vv   AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  T1                            14                               6
  T2                            84                              21
  T3                           320                              97
  T4                            46                              23
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 22(20Q11.21) MUTATED   243 128  93
  AMP PEAK 22(20Q11.21) WILD-TYPE 103  22  22
D22V6, multiclass
    clus
vv   AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  N0                           243                             103
  N1                           128                              22
  N2                            93                              22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q11.21) MUTATED   335  77
  AMP PEAK 22(20Q11.21) WILD-TYPE 118  11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED    335   77
  AMP PEAK 22(20Q11.21) WILD-TYPE  118   11
   clus
vv  AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  0                           335                             118
  1                            77                              11
[1] 2 2
[1] FALSE
D22V8, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q11.21) MUTATED   213 254
  AMP PEAK 22(20Q11.21) WILD-TYPE  76  71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED    213  254
  AMP PEAK 22(20Q11.21) WILD-TYPE   76   71
        clus
vv       AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  FEMALE                           213                              76
  MALE                             254                              71
[1] 2 2
[1] FALSE
D22V9, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q11.21) MUTATED   364  24
  AMP PEAK 22(20Q11.21) WILD-TYPE 118   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED    364   24
  AMP PEAK 22(20Q11.21) WILD-TYPE  118    5
     clus
vv    AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  NO                            364                             118
  YES                            24                               5
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 22(20Q11.21) MUTATED                    291
  AMP PEAK 22(20Q11.21) WILD-TYPE                   91
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(20Q11.21) MUTATED                              26
  AMP PEAK 22(20Q11.21) WILD-TYPE                            36
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 22(20Q11.21) MUTATED                     135
  AMP PEAK 22(20Q11.21) WILD-TYPE                    11
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 22(20Q11.21) MUTATED                                7
  AMP PEAK 22(20Q11.21) WILD-TYPE                              6
D22V10, multiclass
                                clus
vv                               AMP PEAK 22(20Q11.21) MUTATED
  COLON ADENOCARCINOMA                                     291
  COLON MUCINOUS ADENOCARCINOMA                             26
  RECTAL ADENOCARCINOMA                                    135
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 22(20Q11.21) WILD-TYPE
  COLON ADENOCARCINOMA                                        91
  COLON MUCINOUS ADENOCARCINOMA                               36
  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"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 22(20Q11.21) MUTATED   337   5  32  17
  AMP PEAK 22(20Q11.21) WILD-TYPE 109   1   5  12
D22V11, multiclass
    clus
vv   AMP PEAK 22(20Q11.21) MUTATED AMP PEAK 22(20Q11.21) WILD-TYPE
  R0                           337                             109
  R1                             5                               1
  R2                            32                               5
  RX                            17                              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"
D22V12, continuous
D22V13, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q11.21) MUTATED     4 268
  AMP PEAK 22(20Q11.21) WILD-TYPE   1  84
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.21) MUTATED      4  268
  AMP PEAK 22(20Q11.21) WILD-TYPE    1   84
                        clus
vv                       AMP PEAK 22(20Q11.21) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           268
                        clus
vv                       AMP PEAK 22(20Q11.21) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              84
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(20Q12) MUTATION ANALYSIS
D23V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 23(20Q12) MUTATED   359  94
  AMP PEAK 23(20Q12) WILD-TYPE 107  34
  AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE 
                         453                          141 
  AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE 
                          94                           34 
$`AMP PEAK 23(20Q12) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       14.93        31.07        24.03        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       25.08       106.75         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 
       23.51        63.62        35.93        91.79        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE 
       55.76        26.43        15.62         4.80         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.76        43.43        44.91        35.11        16.57 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        34.65        36.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       22.52        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        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3514 
        5.03         7.04         1.02        37.05         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       20.98        13.94        78.08         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 
       47.05        47.01        15.02        37.05         5.03        10.06 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 
        0.00        17.03        10.06        33.07        32.05         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 
       31.07        17.03        27.02        18.05        24.00        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       27.02         7.96        13.94        19.00        34.03        18.05 
TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
        4.01        27.02        42.02        17.03        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01S 
       15.02        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-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       12.16        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 
       16.44         0.46        14.50        16.31         0.95        33.01 
TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
        0.20        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41         5.65         5.13        22.36        65.00        62.79 
TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 
       49.41        12.10        29.56         5.23         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.36        12.46        12.59        12.59        12.20        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 
       17.56       148.01        85.45        21.99         2.01        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       37.02        25.02         8.02        13.02        29.06        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        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-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.08        11.01        10.06        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        55.92        20.19        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49         7.53        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
        9.04        11.64        13.41        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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 
       12.59         7.50        44.32       131.51       139.17        14.04 
TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6459 
       26.47       119.93        35.97       117.07        95.18         8.61 
TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6704 TCGA-F4-6805 
       31.96        35.74        35.74         6.18         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
      133.18         8.35        82.39        74.56        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 
       55.04        39.42        61.91        36.00        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB 
       13.78        46.75        74.79        18.18        19.33        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 
       21.90        38.70        60.13        11.90        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       17.23        43.04        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       36.03         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       29.98        37.02         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        46.03        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
        9.07         1.02         1.02         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        25.05       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         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        4.18        20.55        20.91        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-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       13.64        11.97         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

$`AMP PEAK 23(20Q12) WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
        0.92        19.04        19.04        29.98        24.00         2.01 
TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 
       39.06        10.88        75.95       100.01        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       26.17        79.69        12.66         9.53        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 
       42.28        37.05        32.75        31.63        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       22.06         8.38        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 
       24.92         3.02        35.01        63.98         1.02        29.95 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 
       61.02         6.97        54.02        11.01         5.98        26.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
        1.02        17.98        15.95         0.00         0.00        36.03 
TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 
       53.00        31.00         2.01        33.01        26.01        25.02 
TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 
       27.02        38.04        30.02        18.05         0.99        34.98 
TCGA-AA-A01D TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A02R 
       10.98        38.07         1.02        35.01         1.02        22.03 
TCGA-AA-A03F TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 
       18.05        83.24         0.92        27.09        21.44        17.82 
TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5796 
       58.39        32.94        88.21         6.77        11.74        12.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 
       12.76        10.06        70.16        15.62        51.32        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 
       82.95       124.27        23.05        26.04        27.02        15.02 
TCGA-CM-6162 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 
       12.00        12.95        13.05        12.03        20.42        16.14 
TCGA-D5-6541 TCGA-D5-6927 TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB 
       15.58         9.44        13.35        12.00       140.38       135.65 
TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 
        7.76        81.37        60.79        98.24        11.11        47.87 
TCGA-F4-6856 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-NH-A50U TCGA-NH-A5IV 
       35.31        67.30        53.62        85.48        10.98        19.33 
TCGA-NH-A6GA TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 
        9.93        31.30        70.03        13.55        34.49        12.00 
TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 
       32.02         2.01         6.05        32.98        19.04        13.02 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-DT-5265 TCGA-EI-6507 
        3.98        20.98        49.97        61.97        12.62        19.96 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
        8.61        17.46         8.45 

  AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE 
                           0                            0 
  AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE 
                      148.01                       140.38 
  AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE 
                       22.03                        21.44 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (21.4)"
[1] "hr=" "1.1"
D23V2, continuous
D23V3, binary
                              cls
clus                             0   1
  AMP PEAK 23(20Q12) MUTATED   321 145
  AMP PEAK 23(20Q12) WILD-TYPE 127  17
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(20Q12) MUTATED    321  145
  AMP PEAK 23(20Q12) WILD-TYPE  127   17
        clus
vv       AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE
  COLON                         321                          127
  RECTUM                        145                           17
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 23(20Q12) MUTATED        79        1       22       119         6
  AMP PEAK 23(20Q12) WILD-TYPE      25        0       15        53         6
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(20Q12) MUTATED           2        17         14         68
  AMP PEAK 23(20Q12) WILD-TYPE         0         7          1         16
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 23(20Q12) MUTATED           45       56        23         1
  AMP PEAK 23(20Q12) WILD-TYPE         10        7         1         1
D23V4, multiclass
            clus
vv           AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE
  STAGE I                            79                           25
  STAGE IA                            1                            0
  STAGE II                           22                           15
  STAGE IIA                         119                           53
  STAGE IIB                           6                            6
  STAGE IIC                           2                            0
  STAGE III                          17                            7
  STAGE IIIA                         14                            1
  STAGE IIIB                         68                           16
  STAGE IIIC                         45                           10
  STAGE IV                           56                            7
  STAGE IVA                          23                            1
  STAGE IVB                           1                            1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK 23(20Q12) MUTATED    14  84 321  47
  AMP PEAK 23(20Q12) WILD-TYPE   6  21  96  22
D23V5, multiclass
    clus
vv   AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE
  T1                         14                            6
  T2                         84                           21
  T3                        321                           96
  T4                         47                           22
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  AMP PEAK 23(20Q12) MUTATED   244 129  93
  AMP PEAK 23(20Q12) WILD-TYPE 102  21  22
D23V6, multiclass
    clus
vv   AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE
  N0                        244                          102
  N1                        129                           21
  N2                         93                           22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                              cls
clus                             0   1
  AMP PEAK 23(20Q12) MUTATED   335  79
  AMP PEAK 23(20Q12) WILD-TYPE 118   9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(20Q12) MUTATED    335   79
  AMP PEAK 23(20Q12) WILD-TYPE  118    9
   clus
vv  AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE
  0                        335                          118
  1                         79                            9
[1] 2 2
[1] FALSE
D23V8, binary
                              cls
clus                             0   1
  AMP PEAK 23(20Q12) MUTATED   214 255
  AMP PEAK 23(20Q12) WILD-TYPE  75  70
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(20Q12) MUTATED    214  255
  AMP PEAK 23(20Q12) WILD-TYPE   75   70
        clus
vv       AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE
  FEMALE                        214                           75
  MALE                          255                           70
[1] 2 2
[1] FALSE
D23V9, binary
                              cls
clus                             0   1
  AMP PEAK 23(20Q12) MUTATED   366  24
  AMP PEAK 23(20Q12) WILD-TYPE 116   5
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(20Q12) MUTATED    366   24
  AMP PEAK 23(20Q12) WILD-TYPE  116    5
     clus
vv    AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE
  NO                         366                          116
  YES                         24                            5
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  AMP PEAK 23(20Q12) MUTATED                    293
  AMP PEAK 23(20Q12) WILD-TYPE                   89
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(20Q12) MUTATED                              25
  AMP PEAK 23(20Q12) WILD-TYPE                            37
                              vv
clus                           RECTAL ADENOCARCINOMA
  AMP PEAK 23(20Q12) MUTATED                     136
  AMP PEAK 23(20Q12) WILD-TYPE                    10
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 23(20Q12) MUTATED                                7
  AMP PEAK 23(20Q12) WILD-TYPE                              6
D23V10, multiclass
                                clus
vv                               AMP PEAK 23(20Q12) MUTATED
  COLON ADENOCARCINOMA                                  293
  COLON MUCINOUS ADENOCARCINOMA                          25
  RECTAL ADENOCARCINOMA                                 136
  RECTAL MUCINOUS ADENOCARCINOMA                          7
                                clus
vv                               AMP PEAK 23(20Q12) WILD-TYPE
  COLON ADENOCARCINOMA                                     89
  COLON MUCINOUS ADENOCARCINOMA                            37
  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"
                              vv
clus                            R0  R1  R2  RX
  AMP PEAK 23(20Q12) MUTATED   338   5  32  17
  AMP PEAK 23(20Q12) WILD-TYPE 108   1   5  12
D23V11, multiclass
    clus
vv   AMP PEAK 23(20Q12) MUTATED AMP PEAK 23(20Q12) WILD-TYPE
  R0                        338                          108
  R1                          5                            1
  R2                         32                            5
  RX                         17                           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"
D23V12, continuous
D23V13, binary
                              cls
clus                             0   1
  AMP PEAK 23(20Q12) MUTATED     4 272
  AMP PEAK 23(20Q12) WILD-TYPE   1  80
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 23(20Q12) MUTATED      4  272
  AMP PEAK 23(20Q12) WILD-TYPE    1   80
                        clus
vv                       AMP PEAK 23(20Q12) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        272
                        clus
vv                       AMP PEAK 23(20Q12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           80
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(20Q13.12) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 24(20Q13.12) MUTATED   359  96
  AMP PEAK 24(20Q13.12) WILD-TYPE 107  32
  AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE 
                            455                             139 
  AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE 
                             96                              32 
$`AMP PEAK 24(20Q13.12) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       58.03        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 
       14.93        31.07        24.03        12.99        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 TCGA-AD-6888 
       24.00        19.07        38.04        21.99        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       25.08       106.75         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 
       23.51        63.62        35.93        91.79        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE 
       55.76        26.43        15.62         4.80         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.76        43.43        44.91        35.11        16.57 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        34.65        36.53        32.45        32.91 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       30.44        29.19        23.61        32.71        29.16        27.09 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       22.52        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        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3514 
        5.03         7.04         1.02        37.05         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       20.98        13.94        78.08        54.02         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3696 
       50.04        47.05        47.01        15.02        37.05         5.03 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 
       10.06        35.05         0.99        25.02        38.99        36.95 
TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       37.02         0.00        17.03        10.06        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 
        0.99        31.07        17.03        27.02        18.05        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-3982 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       34.06        27.02         7.96        13.94        19.00        34.03 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        32.02        12.00        31.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
       31.00         1.02        33.04        26.01        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        2.96        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A02Y TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       39.98        40.96        12.16        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       27.42        26.47        16.44         0.46        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
        0.95        33.01         0.20        17.26        17.85        18.84 
TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
      109.28         1.41         5.65         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       62.79        49.41        12.10        29.56         5.23        11.74 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 
        3.19        12.69        12.36        12.46        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-5914 
       12.20        14.30        17.56       148.01        85.45        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        25.02         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        32.02         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 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       17.75        18.25        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
        4.80        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-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H 
      139.17        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        31.96        35.74        35.74         6.18 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
        0.53        47.41       133.18         8.35        82.39        74.56 
TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       65.85        44.68        55.04        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       32.98         8.42        21.90        38.70        60.13        11.90 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       46.92        39.48        17.23        43.04        37.97        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       29.98        16.83        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       65.98        11.84        36.03         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       50.04        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        29.98        37.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        17.95        36.95        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         1.02        46.03        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 
       23.01        37.02         9.07         1.02         1.02         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
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         3.48         4.18        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        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

$`AMP PEAK 24(20Q13.12) WILD-TYPE`
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       13.02        24.03        37.05         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
        0.92        19.04        19.04        29.98        24.00         2.01 
TCGA-AA-A024 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 TCGA-G4-6586 
       39.06        10.88        75.95       100.01        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       26.17        79.69        12.66         9.53        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5664 
       42.28        37.05        32.75        31.63        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
       22.06         8.38        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3555 
       24.92         3.02        35.01        63.98         1.02        29.95 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3710 TCGA-AA-3821 
       61.02         6.97        11.01         5.98        26.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 
       17.98        15.95         0.00         0.00        36.03        53.00 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3977 TCGA-AA-3994 
       31.00         2.01        33.01        26.01        25.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01P 
       38.04        30.02        18.05         0.99        34.98        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A02R TCGA-AA-A03F TCGA-AD-6889 
        1.02        35.01         1.02        22.03        18.05        83.24 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4315 
        0.92        27.09        21.44        17.82        19.33        58.39 
TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 
       32.94        88.21         6.77        12.39        12.76        10.06 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5861 TCGA-CM-6162 TCGA-CM-6674 
       23.05        26.04        27.02        15.02        12.00        12.95 
TCGA-CM-6675 TCGA-CM-6680 TCGA-D5-6530 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6927 
       13.05        12.03        20.42        16.14        15.58         9.44 
TCGA-D5-6930 TCGA-D5-6931 TCGA-DM-A1D9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C 
       13.35        12.00       140.38       135.65         7.76        81.37 
TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6461 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6302 
       60.79        98.24        11.11        47.87        35.31        67.30 
TCGA-G4-6304 TCGA-G4-6309 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-QG-A5Z2 
       53.62        85.48        10.98        19.33         9.93        31.30 
TCGA-WS-AB45 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 
       70.03        13.55        34.49        12.00        32.02         2.01 
TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-4021 TCGA-AG-A002 
        6.05        32.98        19.04        13.02         3.98        20.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 
       49.97        61.97        12.62        19.96         8.61        17.46 
TCGA-EI-7004 
        8.45 

  AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE 
                              0                               0 
  AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE 
                         148.01                          140.38 
  AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE 
                          22.03                           21.44 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (21.4)"
[1] "hr=" "1"  
D24V2, continuous
D24V3, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20Q13.12) MUTATED   323 145
  AMP PEAK 24(20Q13.12) WILD-TYPE 125  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q13.12) MUTATED    323  145
  AMP PEAK 24(20Q13.12) WILD-TYPE  125   17
        clus
vv       AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE
  COLON                            323                             125
  RECTUM                           145                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  AMP PEAK 24(20Q13.12) MUTATED        78        1       23       119         6
  AMP PEAK 24(20Q13.12) WILD-TYPE      26        0       14        53         6
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 24(20Q13.12) MUTATED           2        17         14         68
  AMP PEAK 24(20Q13.12) WILD-TYPE         0         7          1         16
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  AMP PEAK 24(20Q13.12) MUTATED           46       57        23         1
  AMP PEAK 24(20Q13.12) WILD-TYPE          9        6         1         1
D24V4, multiclass
            clus
vv           AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE
  STAGE I                               78                              26
  STAGE IA                               1                               0
  STAGE II                              23                              14
  STAGE IIA                            119                              53
  STAGE IIB                              6                               6
  STAGE IIC                              2                               0
  STAGE III                             17                               7
  STAGE IIIA                            14                               1
  STAGE IIIB                            68                              16
  STAGE IIIC                            46                               9
  STAGE IV                              57                               6
  STAGE IVA                             23                               1
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  AMP PEAK 24(20Q13.12) MUTATED    14  83 323  48
  AMP PEAK 24(20Q13.12) WILD-TYPE   6  22  94  21
D24V5, multiclass
    clus
vv   AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE
  T1                            14                               6
  T2                            83                              22
  T3                           323                              94
  T4                            48                              21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  AMP PEAK 24(20Q13.12) MUTATED   244 129  95
  AMP PEAK 24(20Q13.12) WILD-TYPE 102  21  20
D24V6, multiclass
    clus
vv   AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE
  N0                           244                             102
  N1                           129                              21
  N2                            95                              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"
D24V7, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20Q13.12) MUTATED   336  80
  AMP PEAK 24(20Q13.12) WILD-TYPE 117   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q13.12) MUTATED    336   80
  AMP PEAK 24(20Q13.12) WILD-TYPE  117    8
   clus
vv  AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE
  0                           336                             117
  1                            80                               8
[1] 2 2
[1] FALSE
D24V8, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20Q13.12) MUTATED   215 256
  AMP PEAK 24(20Q13.12) WILD-TYPE  74  69
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q13.12) MUTATED    215  256
  AMP PEAK 24(20Q13.12) WILD-TYPE   74   69
        clus
vv       AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE
  FEMALE                           215                              74
  MALE                             256                              69
[1] 2 2
[1] FALSE
D24V9, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20Q13.12) MUTATED   368  24
  AMP PEAK 24(20Q13.12) WILD-TYPE 114   5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q13.12) MUTATED    368   24
  AMP PEAK 24(20Q13.12) WILD-TYPE  114    5
     clus
vv    AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE
  NO                            368                             114
  YES                            24                               5
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  AMP PEAK 24(20Q13.12) MUTATED                    294
  AMP PEAK 24(20Q13.12) WILD-TYPE                   88
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(20Q13.12) MUTATED                              26
  AMP PEAK 24(20Q13.12) WILD-TYPE                            36
                                 vv
clus                              RECTAL ADENOCARCINOMA
  AMP PEAK 24(20Q13.12) MUTATED                     136
  AMP PEAK 24(20Q13.12) WILD-TYPE                    10
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  AMP PEAK 24(20Q13.12) MUTATED                                7
  AMP PEAK 24(20Q13.12) WILD-TYPE                              6
D24V10, multiclass
                                clus
vv                               AMP PEAK 24(20Q13.12) MUTATED
  COLON ADENOCARCINOMA                                     294
  COLON MUCINOUS ADENOCARCINOMA                             26
  RECTAL ADENOCARCINOMA                                    136
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 24(20Q13.12) WILD-TYPE
  COLON ADENOCARCINOMA                                        88
  COLON MUCINOUS ADENOCARCINOMA                               36
  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"
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 24(20Q13.12) MUTATED   339   5  32  17
  AMP PEAK 24(20Q13.12) WILD-TYPE 107   1   5  12
D24V11, multiclass
    clus
vv   AMP PEAK 24(20Q13.12) MUTATED AMP PEAK 24(20Q13.12) WILD-TYPE
  R0                           339                             107
  R1                             5                               1
  R2                            32                               5
  RX                            17                              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"
D24V12, continuous
D24V13, binary
                                 cls
clus                                0   1
  AMP PEAK 24(20Q13.12) MUTATED     4 272
  AMP PEAK 24(20Q13.12) WILD-TYPE   1  80
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 24(20Q13.12) MUTATED      4  272
  AMP PEAK 24(20Q13.12) WILD-TYPE    1   80
                        clus
vv                       AMP PEAK 24(20Q13.12) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           272
                        clus
vv                       AMP PEAK 24(20Q13.12) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                              80
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.11) MUTATED   176  57
  DEL PEAK  1(1P36.11) WILD-TYPE 290  71
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                           233                            361 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            57                             71 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3531 
       24.33        13.94        14.53        37.05        19.07        34.03 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       13.02        23.01        19.99        19.00        36.00        85.05 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 
       31.07        24.03        29.98        12.99         2.01        50.99 
TCGA-AA-3976 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6625 TCGA-AF-3913 
       26.01         5.88        23.51        35.93        91.79        10.39 
TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6641 TCGA-4N-A93T 
       17.03        25.97        51.98        21.24        26.43         4.80 
TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3810 
        1.61        43.76        44.91        35.11        16.57        36.53 
TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 
       32.45        29.19        23.61        32.71        29.16        22.52 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B TCGA-AA-3488 
       24.13        25.18        21.76        23.87        56.25         5.03 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3666 
       38.99         9.07        19.07        14.01        24.00         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3819 
       14.01        50.04        47.01        37.05        10.06        25.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 
       38.99        36.95        37.02        10.06        33.07        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 
        0.99        31.07        17.03         2.01         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A017 TCGA-AA-A01C 
       13.05         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        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       22.42        26.47        16.44         0.46        14.50        16.31 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-6600 
       17.85         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        12.69        12.36        12.46 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 
       12.59        12.59        12.20        14.30        21.99         2.01 
TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 
       25.02         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        45.40        56.09        20.19 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6541 
       17.75        25.48        43.27        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-A28A TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6460 
       44.32       139.17        26.47       117.07        95.18        31.96 
TCGA-F4-6461 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6855 TCGA-G4-6295 
       11.11         1.55        41.42        13.25        47.41         8.35 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T 
       82.39        65.85        61.91        36.00        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-SS-A7HO TCGA-T9-A92H 
       10.98         9.93        16.80        42.77        60.13        11.90 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
       46.92        17.23        43.04        13.55        37.97        29.98 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 
       24.36        86.63        65.98        11.84        32.02        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3609 
       20.05        24.00        46.03        34.03         6.05        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
        0.99        29.98        37.02        19.04        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 
       36.95         1.02        48.03        25.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       36.03        13.94        23.01         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       38.56        43.20        27.55        13.78        44.78        48.20 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       25.05        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 
       44.02        25.97        25.05       126.44       129.27        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 TCGA-EI-7004 
        3.48         4.18        20.55        15.85        11.97         8.45 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6572 
       28.57        32.19        19.66        12.46        47.08 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       45.60        24.16         1.02        58.03        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3662 
       36.03         8.05         0.99        17.95        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3950 TCGA-AA-3979 
        0.92        19.04        19.04        14.93        24.00        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       49.08        28.21        63.62        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 
       79.69        17.85         8.02        13.94        19.99        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B 
       15.95        36.03        31.00        18.28        55.76        15.62 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 
       12.66         9.53        39.45        43.76        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       42.90        42.28        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       32.75        32.91        31.63        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6652 
       22.06        27.09         8.38        25.08        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84         9.63         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 
       35.01        63.98         6.97         1.02         1.02         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        26.01        12.99        33.99        21.01 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       54.02        47.05        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 
        0.00        17.03         0.00         0.00        36.03        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       27.02        18.05        31.00        24.00        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       20.98        34.03        16.08        34.06        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W 
       18.05         4.01        27.02         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       34.98        10.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O 
       35.01         1.02         1.02        37.02        51.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6963 
       22.03        39.98        18.05        12.16        83.24        27.42 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
        0.92        27.09         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        1.41        32.94        62.79        88.21        49.41         6.77 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       11.74        12.39        12.76        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 
       85.45        70.16        15.62        51.32        21.14        82.95 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        20.02        37.02        26.04        27.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 
       29.06        22.98        32.02        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-6171 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5538 
       14.04        12.95        13.05        11.08        11.01        54.61 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6537 TCGA-D5-6538 
       19.59        55.92        20.42        18.25         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6926 
       12.49        16.14         7.53        12.39        10.13         9.04 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       24.43        38.20       130.65        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C 
        7.50       131.51       135.65         7.76        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6463 
      119.93        35.97        60.79        98.24         8.61        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6808 
       35.74         6.18        47.87        34.42        43.04        33.67 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
        0.53        35.31       133.18        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 
       44.68        55.04        85.48        39.42        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       13.78        74.79        19.33        19.33        15.65        12.79 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        38.70 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 
       70.03        39.48        34.49        37.74        16.83        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3591 
       24.59        36.03        12.00         7.07         1.02        34.03 
TCGA-AG-3592 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-3725 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3885 
       20.98         7.99        32.98         0.99         0.99        17.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 
       13.02        35.01        14.01        32.02        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 
        3.98        46.03        20.98         6.02        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
        1.02         1.02        49.97        61.97        41.00         2.50 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-5917 
       26.43        19.46         6.05        33.17        47.44        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 
        7.17        21.01        26.04        10.98        25.05        12.62 
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 
       49.51        42.35         0.39        36.49        37.18        38.14 
TCGA-F5-6863 
       11.87 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        139.17                         148.01 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         23.51                          21.01 
[1] "0.5 - 139.2 (23.5)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.3"
D25V2, continuous
D25V3, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   167  73
  DEL PEAK  1(1P36.11) WILD-TYPE 281  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    167   73
  DEL PEAK  1(1P36.11) WILD-TYPE  281   89
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  COLON                           167                            281
  RECTUM                           73                             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        9        63         4
  DEL PEAK  1(1P36.11) WILD-TYPE      71        1       28       109         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  1(1P36.11) MUTATED           1         8          7         31
  DEL PEAK  1(1P36.11) WILD-TYPE         1        16          8         53
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  1(1P36.11) MUTATED           26       38        15         0
  DEL PEAK  1(1P36.11) WILD-TYPE         29       25         9         2
D25V4, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              33                             71
  STAGE IA                              0                              1
  STAGE II                              9                             28
  STAGE IIA                            63                            109
  STAGE IIB                             4                              8
  STAGE IIC                             1                              1
  STAGE III                             8                             16
  STAGE IIIA                            7                              8
  STAGE IIIB                           31                             53
  STAGE IIIC                           26                             29
  STAGE IV                             38                             25
  STAGE IVA                            15                              9
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  1(1P36.11) MUTATED     5  40 164  33
  DEL PEAK  1(1P36.11) WILD-TYPE  15  65 253  36
D25V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            5                             15
  T2                           40                             65
  T3                          164                            253
  T4                           33                             36
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK  1(1P36.11) MUTATED   118  65  58
  DEL PEAK  1(1P36.11) WILD-TYPE 228  85  57
D25V6, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                          118                            228
  N1                           65                             85
  N2                           58                             57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   164  53
  DEL PEAK  1(1P36.11) WILD-TYPE 289  35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    164   53
  DEL PEAK  1(1P36.11) WILD-TYPE  289   35
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                          164                            289
  1                           53                             35
[1] 2 2
[1] FALSE
D25V8, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   105 138
  DEL PEAK  1(1P36.11) WILD-TYPE 184 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    105  138
  DEL PEAK  1(1P36.11) WILD-TYPE  184  187
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                          105                            184
  MALE                            138                            187
[1] 2 2
[1] FALSE
D25V9, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED   191  13
  DEL PEAK  1(1P36.11) WILD-TYPE 291  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED    191   13
  DEL PEAK  1(1P36.11) WILD-TYPE  291   16
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                           191                            291
  YES                           13                             16
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                    155
  DEL PEAK  1(1P36.11) WILD-TYPE                  227
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                              11
  DEL PEAK  1(1P36.11) WILD-TYPE                            51
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK  1(1P36.11) MUTATED                      65
  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
D25V10, multiclass
                                clus
vv                               DEL PEAK  1(1P36.11) MUTATED
  COLON ADENOCARCINOMA                                    155
  COLON MUCINOUS ADENOCARCINOMA                            11
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK  1(1P36.11) WILD-TYPE
  COLON ADENOCARCINOMA                                      227
  COLON MUCINOUS ADENOCARCINOMA                              51
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  1(1P36.11) MUTATED   166   3  21  12
  DEL PEAK  1(1P36.11) WILD-TYPE 280   3  16  17
D25V11, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                          166                            280
  R1                            3                              3
  R2                           21                             16
  RX                           12                             17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V12, continuous
D25V13, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.11) MUTATED     2 138
  DEL PEAK  1(1P36.11) WILD-TYPE   3 214
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      2  138
  DEL PEAK  1(1P36.11) WILD-TYPE    3  214
                        clus
vv                       DEL PEAK  1(1P36.11) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          138
                        clus
vv                       DEL PEAK  1(1P36.11) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            214
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  2(1P33) MUTATION ANALYSIS
D26V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1P33) MUTATED   122  46
  DEL PEAK  2(1P33) WILD-TYPE 344  82
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                        168                         426 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         46                          82 
$`DEL PEAK  2(1P33) MUTATED`
TCGA-A6-4105 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 
       14.53        37.05         8.05        19.99        19.00        85.05 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3939 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6625 
       31.07        24.03        12.99        23.51        35.93        91.79 
TCGA-AG-A00H TCGA-BM-6198 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-A6-2674 TCGA-A6-2680 
       25.97        21.24         4.80         1.61        43.76        35.11 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5660 
       16.57        37.25        37.02        36.53        32.45        29.19 
TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6654 TCGA-AA-3488 
       23.61        29.16        22.52        21.76        23.87         5.03 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3549 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 
       38.99         9.07        21.01        50.04        37.05        10.06 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3851 
       38.99        36.95        37.02         0.00        10.06        33.07 
TCGA-AA-3855 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 
       32.05        17.03         2.01         2.01        21.99        13.05 
TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
        7.96        34.03        42.02        15.02        32.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02R TCGA-AA-A02W 
       33.04        26.01         2.96         2.01        22.03        41.00 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
       24.53         5.79        22.42        26.47        16.44        14.50 
TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-5403 TCGA-AZ-6600 
       16.31        17.85         5.65         5.13        62.79        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        12.69        12.36        12.46 
TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 
       12.20         2.01         8.02        13.02        22.03         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 
       15.02        14.04        29.03        13.02        15.02        11.08 
TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-5540 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       11.08        10.06        56.09        25.48        15.12        17.85 
TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 
       14.30        13.41        11.38        38.20        92.75        49.91 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6855 
       14.04        26.47        35.97        31.96         1.55        47.41 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
        8.35        82.39        65.85        61.91        36.00        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-SS-A7HO 
       18.18        10.98         9.93        16.80        42.77        60.13 
TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 
       11.90        46.92        17.23        13.55        29.98        24.36 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 
       86.63        65.98        11.84        32.02        36.03        24.00 
TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 
       34.03        29.98        37.02        19.04        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00Y TCGA-AG-A026 
       48.03        19.99        28.04        36.03        23.01         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6621 TCGA-CI-6623 
       38.96        38.04        38.56        43.20        13.78        47.44 
TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       48.20        21.01        25.05        31.00        13.97        51.98 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 
       44.02       126.44       129.27         3.48        20.55        15.85 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6572 
       13.64        11.97        28.57        32.19        19.66        47.08 

$`DEL PEAK  2(1P33) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       13.02        24.03        36.03        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 
       13.02        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3950 
       36.00        19.04        19.04        14.93        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       28.21        63.62        22.09        35.80        26.17        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       17.85        10.39         8.02        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 
       17.03        15.95        36.03        31.00        51.98        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE 
       55.76        26.43        15.62        12.66         9.53        39.45 
TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       43.76        46.65        43.43        42.90        42.28        44.91 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.05        34.65        32.75        32.91        31.63        30.44 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 
       33.53        22.09        22.06        32.71        27.09        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        20.61        24.69        24.39 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       56.25         9.63         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 
       35.01        63.98         6.97         1.02         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       78.08         6.97        54.02         2.01        14.01        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
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-3846 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
       17.03         0.00         0.00        36.03         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
       53.00        27.02        18.05        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
       26.01        20.98        34.03        16.08        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        27.02        13.94        38.04        19.00        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-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       14.99        34.98        15.02        10.98        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         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
       51.98        39.98         5.03         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 
       40.96        12.16        83.24        27.42         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       32.94        22.36        65.00        88.21        49.41         6.77 
TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       11.74        12.39        12.59        12.59        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14        82.95       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        25.02        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        32.02        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-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 
       45.40        54.61        19.59        55.92        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        43.27         4.80        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        13.35        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-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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 
        8.61        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        74.56        67.30        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       55.04        85.48        39.42        26.43        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YW 
       74.79        19.33        19.33        15.65        12.79        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        38.70        70.03 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       39.48        43.04        37.97        34.49        37.74        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 
       20.02        24.59        36.03        12.00         7.07        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
        1.02        46.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        7.99         0.99        32.98         0.99         0.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 
       17.95        36.95        13.02        35.01        14.01        25.02 
TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       32.02        14.04         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       49.97        61.97        41.00         2.50        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
       19.46         6.05        33.17        44.78        78.12         7.17 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
       26.04        12.00        31.00        10.98        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       25.05        12.62        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61         4.18        19.96        20.91        17.00        18.28 
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-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        17.46         8.45         9.96        49.51        42.35 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.39        36.49        37.18        38.14        11.87        12.46 

  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                          0                           0 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                     129.27                      148.01 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                     22.765                      21.670 
[1] "0.0 - 129.3 (22.8)" "0.0 - 148.0 (21.7)"
[1] "hr=" "1.5"
D26V2, continuous
D26V3, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   123  51
  DEL PEAK  2(1P33) WILD-TYPE 325 111
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    123   51
  DEL PEAK  2(1P33) WILD-TYPE  325  111
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  COLON                        123                         325
  RECTUM                        51                         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        8        50         2
  DEL PEAK  2(1P33) WILD-TYPE      85        1       29       122        10
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  2(1P33) MUTATED           0         5          4         25
  DEL PEAK  2(1P33) WILD-TYPE         2        19         11         59
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  2(1P33) MUTATED           21       29         6         0
  DEL PEAK  2(1P33) WILD-TYPE         34       34        18         2
D26V4, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                           19                          85
  STAGE IA                           0                           1
  STAGE II                           8                          29
  STAGE IIA                         50                         122
  STAGE IIB                          2                          10
  STAGE IIC                          0                           2
  STAGE III                          5                          19
  STAGE IIIA                         4                          11
  STAGE IIIB                        25                          59
  STAGE IIIC                        21                          34
  STAGE IV                          29                          34
  STAGE IVA                          6                          18
  STAGE IVB                          0                           2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  2(1P33) MUTATED     4  23 126  22
  DEL PEAK  2(1P33) WILD-TYPE  16  82 291  47
D26V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T1                         4                          16
  T2                        23                          82
  T3                       126                         291
  T4                        22                          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  2(1P33) MUTATED    85  51  39
  DEL PEAK  2(1P33) WILD-TYPE 261  99  76
D26V6, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        85                         261
  N1                        51                          99
  N2                        39                          76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   120  35
  DEL PEAK  2(1P33) WILD-TYPE 333  53
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    120   35
  DEL PEAK  2(1P33) WILD-TYPE  333   53
   clus
vv  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  0                       120                         333
  1                        35                          53
[1] 2 2
[1] FALSE
D26V8, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED    79  97
  DEL PEAK  2(1P33) WILD-TYPE 210 228
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     79   97
  DEL PEAK  2(1P33) WILD-TYPE  210  228
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        79                         210
  MALE                          97                         228
[1] 2 2
[1] FALSE
D26V9, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED   140   9
  DEL PEAK  2(1P33) WILD-TYPE 342  20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED    140    9
  DEL PEAK  2(1P33) WILD-TYPE  342   20
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                        140                         342
  YES                         9                          20
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                    113
  DEL PEAK  2(1P33) WILD-TYPE                  269
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                               9
  DEL PEAK  2(1P33) WILD-TYPE                            53
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK  2(1P33) MUTATED                      49
  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
D26V10, multiclass
                                clus
vv                               DEL PEAK  2(1P33) MUTATED
  COLON ADENOCARCINOMA                                 113
  COLON MUCINOUS ADENOCARCINOMA                          9
  RECTAL ADENOCARCINOMA                                 49
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  2(1P33) WILD-TYPE
  COLON ADENOCARCINOMA                                   269
  COLON MUCINOUS ADENOCARCINOMA                           53
  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"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  2(1P33) MUTATED   117   3  14   8
  DEL PEAK  2(1P33) WILD-TYPE 329   3  23  21
D26V11, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                       117                         329
  R1                         3                           3
  R2                        14                          23
  RX                         8                          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"
D26V12, continuous
D26V13, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED     3 103
  DEL PEAK  2(1P33) WILD-TYPE   2 249
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED      3  103
  DEL PEAK  2(1P33) WILD-TYPE    2  249
                        clus
vv                       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  HISPANIC OR LATINO                             3                           2
  NOT HISPANIC OR LATINO                       103                         249
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  3(1P13.2) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(1P13.2) MUTATED   122  46
  DEL PEAK  3(1P13.2) WILD-TYPE 344  82
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                          168                           426 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           46                            82 
$`DEL PEAK  3(1P13.2) MUTATED`
TCGA-A6-4105 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3860 
       14.53        24.03        37.05        19.99        19.00        31.07 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3952 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6625 
       24.03        12.99         2.01         5.88        23.51        91.79 
TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-A6-2671 
       25.97        21.24        18.28         4.80         1.61        43.76 
TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-3810 TCGA-A6-4107 
       43.76        35.11        16.57        37.25        36.53        32.45 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A56B 
       29.19        23.61        22.52        21.76        23.87        56.25 
TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3673 
        5.03        38.99         9.07        21.01        13.94        50.04 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3855 
       37.05        10.06        38.99        37.02        10.06        32.05 
TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3989 
       17.03         2.01         2.01        21.99        13.05         7.96 
TCGA-AA-A00A TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q 
       38.04        42.02        15.02        32.02        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AA-A03J 
       33.04        26.01         2.96         2.01        41.00        40.96 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5821 
       24.53         5.79        22.42        26.47        16.44         0.92 
TCGA-AU-3779 TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 
       14.50        17.85         5.65        32.94         5.13        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       12.10        29.56         5.23         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 
       12.46        12.20         2.01         8.02        13.02        22.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6679 
       14.04        29.03        13.02        15.02        11.08        10.06 
TCGA-D5-5540 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 
       56.09        17.75        25.48        15.12        14.30        13.41 
TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28A 
       11.38        92.75        49.91       131.51        14.04        26.47 
TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 
       31.96         1.55        43.04        33.67        47.41         8.35 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T 
       82.39        65.85        61.91        36.00        46.75        18.18 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-SS-A7HO TCGA-T9-A92H 
       10.98         9.93        16.80        42.77        60.13        11.90 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L 
       46.92        17.23        13.55        29.98        24.36        65.98 
TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 
       11.84        32.02        36.03        24.00        34.03         2.01 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3909 
       29.98        37.02        19.04        19.99         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A032 
       28.04        36.03         3.98        23.01         1.94        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
       38.56        43.20        47.44        25.05        31.00        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5830 
       51.98        44.02       126.44        41.36       129.27         3.48 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 
       20.55        17.00        15.85        11.51        13.64        11.97 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
       28.57        32.19        36.49        19.66        11.87        47.08 

$`DEL PEAK  3(1P13.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       13.02        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 
       13.02        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 
       36.00        85.05        19.04        19.04        14.93        29.98 
TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       24.00        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 
       75.95       106.75       100.01         1.94        49.08        28.21 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       63.62        35.93        22.09        35.80        26.17        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       17.85        10.39         8.02        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
       17.03        15.95        36.03        31.00        51.98        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
       26.43        15.62        12.66         9.53        39.45        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2684 TCGA-A6-2686 
       43.43        42.90        42.28        44.91        37.05        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 
       34.65        32.75        32.91        31.63        30.44        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-A6-6650 TCGA-A6-6652 TCGA-A6-6653 
        8.38        25.08        25.18        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-3502 
        9.63         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
       63.98         6.97         1.02         1.02        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        29.95        20.98        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.98         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        36.95         0.00 
TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       17.03         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       31.07        53.00        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 
       33.01        26.01        20.98        34.03        16.08        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00E 
       25.02        27.02        27.02        13.94        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R 
       34.03        18.05        18.05         4.01        27.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G 
       17.03        14.99        34.98        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z 
       31.00        38.07        35.01         1.02         1.02        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6963 TCGA-AM-5820 TCGA-AU-6004 
       18.05        12.16        83.24        27.42         0.46        27.09 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       16.31         0.95        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 
       22.36        62.79        88.21        49.41         6.77        11.74 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95       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        25.02        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        32.02        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        45.40        54.61        19.59        55.92 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.19        20.42        18.25        43.27        17.85         4.80 
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        13.35 
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        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 
       35.74         6.18        47.87        34.42        41.42        13.25 
TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
        0.53        35.31       133.18        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 
       44.68        55.04        85.48        39.42        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       13.78        74.79        19.33        19.33        15.65        12.79 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        38.70 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       70.03        39.48        43.04        37.97        34.49        37.74 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 
       16.83        20.02        24.59        86.63        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
        7.07        20.05         1.02        46.03        34.03        34.03 
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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       20.98         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       48.03        25.02        32.02        14.04         1.02        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        13.94         6.02        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
        1.02        49.97        38.96        61.97        41.00         2.50 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
       44.78        48.20        78.12         7.17        21.01        26.04 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       12.00        31.00        10.98        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       12.62        57.24        24.13        51.48        32.61         4.18 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       19.96        20.91        18.28        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       16.41         8.61        10.78        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       49.51        42.35         0.39        37.18        38.14        12.46 

  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                         0.92                          0.00 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                       131.51                        148.01 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                       22.225                        21.990 
[1] "0.9 - 131.5 (22.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D27V2, continuous
D27V3, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED   121  52
  DEL PEAK  3(1P13.2) WILD-TYPE 327 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED    121   52
  DEL PEAK  3(1P13.2) WILD-TYPE  327  110
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  COLON                          121                           327
  RECTUM                          52                           110
[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        48         2
  DEL PEAK  3(1P13.2) WILD-TYPE      85        1       29       124        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  3(1P13.2) MUTATED           1         5          4         23
  DEL PEAK  3(1P13.2) WILD-TYPE         1        19         11         61
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  3(1P13.2) MUTATED           22       30         6         0
  DEL PEAK  3(1P13.2) WILD-TYPE         33       33        18         2
D27V4, multiclass
            clus
vv           DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  STAGE I                             19                            85
  STAGE IA                             0                             1
  STAGE II                             8                            29
  STAGE IIA                           48                           124
  STAGE IIB                            2                            10
  STAGE IIC                            1                             1
  STAGE III                            5                            19
  STAGE IIIA                           4                            11
  STAGE IIIB                          23                            61
  STAGE IIIC                          22                            33
  STAGE IV                            30                            33
  STAGE IVA                            6                            18
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  3(1P13.2) MUTATED     5  21 125  23
  DEL PEAK  3(1P13.2) WILD-TYPE  15  84 292  46
D27V5, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  T1                           5                            15
  T2                          21                            84
  T3                         125                           292
  T4                          23                            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  3(1P13.2) MUTATED    84  46  44
  DEL PEAK  3(1P13.2) WILD-TYPE 262 104  71
D27V6, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  N0                          84                           262
  N1                          46                           104
  N2                          44                            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"
D27V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED   121  36
  DEL PEAK  3(1P13.2) WILD-TYPE 332  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED    121   36
  DEL PEAK  3(1P13.2) WILD-TYPE  332   52
   clus
vv  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  0                         121                           332
  1                          36                            52
[1] 2 2
[1] FALSE
D27V8, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED    78  97
  DEL PEAK  3(1P13.2) WILD-TYPE 211 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     78   97
  DEL PEAK  3(1P13.2) WILD-TYPE  211  228
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  FEMALE                          78                           211
  MALE                            97                           228
[1] 2 2
[1] FALSE
D27V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED   139   9
  DEL PEAK  3(1P13.2) WILD-TYPE 343  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED    139    9
  DEL PEAK  3(1P13.2) WILD-TYPE  343   20
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  NO                          139                           343
  YES                           9                            20
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                    111
  DEL PEAK  3(1P13.2) WILD-TYPE                  271
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                              10
  DEL PEAK  3(1P13.2) WILD-TYPE                            52
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                      49
  DEL PEAK  3(1P13.2) WILD-TYPE                    97
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  3(1P13.2) MUTATED                                2
  DEL PEAK  3(1P13.2) WILD-TYPE                             11
D27V10, multiclass
                                clus
vv                               DEL PEAK  3(1P13.2) MUTATED
  COLON ADENOCARCINOMA                                   111
  COLON MUCINOUS ADENOCARCINOMA                           10
  RECTAL ADENOCARCINOMA                                   49
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK  3(1P13.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     271
  COLON MUCINOUS ADENOCARCINOMA                             52
  RECTAL ADENOCARCINOMA                                     97
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  3(1P13.2) MUTATED   118   2  14   9
  DEL PEAK  3(1P13.2) WILD-TYPE 328   4  23  20
D27V11, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  R0                         118                           328
  R1                           2                             4
  R2                          14                            23
  RX                           9                            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"
D27V12, continuous
D27V13, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED     2 104
  DEL PEAK  3(1P13.2) WILD-TYPE   3 248
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED      2  104
  DEL PEAK  3(1P13.2) WILD-TYPE    3  248
                        clus
vv                       DEL PEAK  3(1P13.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                         104
                        clus
vv                       DEL PEAK  3(1P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           248
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  4(2P12) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2P12) MUTATED    18   3
  DEL PEAK  4(2P12) WILD-TYPE 448 125
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         21                         573 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                          3                         125 
$`DEL PEAK  4(2P12) MUTATED`
TCGA-A6-2677 TCGA-AA-3560 TCGA-AA-3939 TCGA-AG-3611 TCGA-AG-A00H TCGA-AA-3511 
       24.33        19.99        12.99        13.94        25.97         6.97 
TCGA-AA-3842 TCGA-AA-A01S TCGA-CM-5341 TCGA-G4-6626 TCGA-AF-6136 TCGA-AG-3578 
       37.02         1.02        29.06        46.75        24.36        32.02 
TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3881 TCGA-AG-3896 TCGA-AG-3999 
       36.03         6.05        19.99        19.04         1.02        28.04 
TCGA-AG-A02X TCGA-DC-6156 TCGA-F5-6571 
       41.00        31.00        42.35 

$`DEL PEAK  4(2P12) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 
       19.04        14.93        31.07        24.03        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       19.99        17.03        17.03        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       51.98        21.24        18.28        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
        4.80        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       35.11        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       32.75        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-A6-6650 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-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       37.05        35.01        63.98         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        2.01        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       11.01         5.98        37.05         5.03        26.99        10.06 
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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        36.95         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
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-A010 TCGA-AA-A017 TCGA-AA-A01C 
        0.99        17.03        14.99        34.98        15.02        15.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       10.98        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01        33.04         1.02        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-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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       83.24        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         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        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.59        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         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        25.02        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        32.02        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        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       54.61        19.59        56.09        55.92        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        25.48        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        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        13.35        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-A288 TCGA-DM-A28A TCGA-DM-A28C 
      135.65         7.76       139.17        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        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.04        13.78        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       60.13        11.90        70.03        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       16.83        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       36.03        12.00         7.07        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98        37.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        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        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       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-6507 
       51.48        32.61         3.48         4.18        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        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                       1.02                        0.00 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                      46.75                      148.01 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                      24.36                       21.99 
[1] "1.0 - 46.8 (24.4)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D28V2, continuous
D28V3, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     8  13
  DEL PEAK  4(2P12) WILD-TYPE 440 149
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      8   13
  DEL PEAK  4(2P12) WILD-TYPE  440  149
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  COLON                          8                         440
  RECTUM                        13                         149
[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     102        1       36       165        12
                             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         2        23         13         83
                             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         50       62        23         2
D28V4, multiclass
            clus
vv           DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  STAGE I                            2                         102
  STAGE IA                           0                           1
  STAGE II                           1                          36
  STAGE IIA                          7                         165
  STAGE IIB                          0                          12
  STAGE IIC                          0                           2
  STAGE III                          1                          23
  STAGE IIIA                         2                          13
  STAGE IIIB                         1                          83
  STAGE IIIC                         5                          50
  STAGE IV                           1                          62
  STAGE IVA                          1                          23
  STAGE IVB                          0                           2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK  4(2P12) MUTATED     0   4  15   2
  DEL PEAK  4(2P12) WILD-TYPE  20 101 402  67
D28V5, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  T1                         0                          20
  T2                         4                         101
  T3                        15                         402
  T4                         2                          67
[1] 4 2
[1] TRUE
[1] "dimension 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 336 145 109
D28V6, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  N0                        10                         336
  N1                         5                         145
  N2                         6                         109
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    18   2
  DEL PEAK  4(2P12) WILD-TYPE 435  86
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     18    2
  DEL PEAK  4(2P12) WILD-TYPE  435   86
   clus
vv  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  0                        18                         435
  1                         2                          86
[1] 2 2
[1] FALSE
D28V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    11  10
  DEL PEAK  4(2P12) WILD-TYPE 278 315
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     11   10
  DEL PEAK  4(2P12) WILD-TYPE  278  315
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  FEMALE                        11                         278
  MALE                          10                         315
[1] 2 2
[1] FALSE
D28V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    15   3
  DEL PEAK  4(2P12) WILD-TYPE 467  26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     15    3
  DEL PEAK  4(2P12) WILD-TYPE  467   26
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  NO                         15                         467
  YES                         3                          26
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                      8
  DEL PEAK  4(2P12) WILD-TYPE                  374
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                               0
  DEL PEAK  4(2P12) WILD-TYPE                            62
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                      11
  DEL PEAK  4(2P12) WILD-TYPE                   135
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  4(2P12) MUTATED                                1
  DEL PEAK  4(2P12) WILD-TYPE                             12
D28V10, 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                                   374
  COLON MUCINOUS ADENOCARCINOMA                           62
  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"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(2P12) MUTATED    18   0   1   0
  DEL PEAK  4(2P12) WILD-TYPE 428   6  36  29
D28V11, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  R0                        18                         428
  R1                         0                           6
  R2                         1                          36
  RX                         0                          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"
D28V12, continuous
D28V13, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     0   6
  DEL PEAK  4(2P12) WILD-TYPE   5 346
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      0    6
  DEL PEAK  4(2P12) WILD-TYPE    5  346
                        clus
vv                       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  HISPANIC OR LATINO                             0                           5
  NOT HISPANIC OR LATINO                         6                         346
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  5(2Q22.1) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(2Q22.1) MUTATED    27   7
  DEL PEAK  5(2Q22.1) WILD-TYPE 439 121
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                           34                           560 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                            7                           121 
$`DEL PEAK  5(2Q22.1) MUTATED`
TCGA-AA-3522 TCGA-AA-3560 TCGA-AA-3939 TCGA-AG-3611 TCGA-AG-A00H TCGA-AG-A014 
       37.05        19.99        12.99        13.94        25.97        15.95 
TCGA-A6-2678 TCGA-A6-3810 TCGA-A6-6651 TCGA-A6-A566 TCGA-AA-3511 TCGA-AA-3666 
       42.28        36.53        21.76        24.92         6.97         2.01 
TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3941 TCGA-AZ-4308 
       15.02        10.06        37.02        10.06        24.00       109.28 
TCGA-CA-5254 TCGA-CA-5797 TCGA-DM-A1D6 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28H 
       12.69        12.59        49.91        44.32       131.51       117.07 
TCGA-F4-6704 TCGA-G4-6626 TCGA-AF-A56L TCGA-AG-3609 TCGA-AG-3881 TCGA-AG-4001 
        1.55        46.75        65.98        19.99        19.04        36.03 
TCGA-AG-A02X TCGA-DC-6682 TCGA-F5-6571 TCGA-F5-6814 
       41.00        25.05        42.35        37.18 

$`DEL PEAK  5(2Q22.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       58.03        13.02        24.03        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 
       19.04        14.93        31.07        24.03        29.98        24.00 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
        2.01        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       19.99        17.03        17.03        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.43        42.90        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 
       37.05        37.25        37.02        34.65        32.75        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-A6-6652 
       24.13         8.38        25.08        25.18        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-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 
        1.02        37.05        35.01        63.98         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 
       26.01        12.99        14.01        33.99        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 
       54.02        14.01        50.04        47.05        47.01        11.01 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       18.05        31.00         2.01        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         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-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        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-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         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        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5256 
       29.56         5.23        11.74         3.19        12.36        12.46 
TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         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        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
       13.02        29.06        22.03        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       15.02         5.03        15.02        15.02        17.03        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-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 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       20.42        17.75        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        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        13.35        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-A1HB TCGA-DM-A280 
       13.32        12.59       140.38         7.50       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
       60.79        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T 
       36.00        26.43        26.04        13.78        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       21.90        38.70        60.13        11.90        70.03        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        29.98        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        11.84        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-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        28.04        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        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        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       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-6507 
       51.48        32.61         3.48         4.18        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        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19        36.49        19.66        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                         1.55                          0.00 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                       131.51                        148.01 
  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE 
                       24.985                        21.990 
[1] "1.6 - 131.5 (25.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D29V2, continuous
D29V3, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    24  11
  DEL PEAK  5(2Q22.1) WILD-TYPE 424 151
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     24   11
  DEL PEAK  5(2Q22.1) WILD-TYPE  424  151
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  COLON                           24                           424
  RECTUM                          11                           151
[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     102        1       36       157        12
                               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         2        22         14         80
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  5(2Q22.1) MUTATED            7        2         1         0
  DEL PEAK  5(2Q22.1) WILD-TYPE         48       61        23         2
D29V4, multiclass
            clus
vv           DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  STAGE I                              2                           102
  STAGE IA                             0                             1
  STAGE II                             1                            36
  STAGE IIA                           15                           157
  STAGE IIB                            0                            12
  STAGE IIC                            0                             2
  STAGE III                            2                            22
  STAGE IIIA                           1                            14
  STAGE IIIB                           4                            80
  STAGE IIIC                           7                            48
  STAGE IV                             2                            61
  STAGE IVA                            1                            23
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  5(2Q22.1) MUTATED     0   3  28   4
  DEL PEAK  5(2Q22.1) WILD-TYPE  20 102 389  65
D29V5, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  T1                           0                            20
  T2                           3                           102
  T3                          28                           389
  T4                           4                            65
[1] 4 2
[1] TRUE
[1] "dimension 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   9
  DEL PEAK  5(2Q22.1) WILD-TYPE 328 142 106
D29V6, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  N0                          18                           328
  N1                           8                           142
  N2                           9                           106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    30   3
  DEL PEAK  5(2Q22.1) WILD-TYPE 423  85
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     30    3
  DEL PEAK  5(2Q22.1) WILD-TYPE  423   85
   clus
vv  DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  0                          30                           423
  1                           3                            85
[1] 2 2
[1] FALSE
D29V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    15  20
  DEL PEAK  5(2Q22.1) WILD-TYPE 274 305
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     15   20
  DEL PEAK  5(2Q22.1) WILD-TYPE  274  305
        clus
vv       DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  FEMALE                          15                           274
  MALE                            20                           305
[1] 2 2
[1] FALSE
D29V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED    25   1
  DEL PEAK  5(2Q22.1) WILD-TYPE 457  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED     25    1
  DEL PEAK  5(2Q22.1) WILD-TYPE  457   28
     clus
vv    DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  NO                           25                           457
  YES                           1                            28
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                     21
  DEL PEAK  5(2Q22.1) WILD-TYPE                  361
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                               3
  DEL PEAK  5(2Q22.1) WILD-TYPE                            59
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                      10
  DEL PEAK  5(2Q22.1) WILD-TYPE                   136
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  5(2Q22.1) MUTATED                                0
  DEL PEAK  5(2Q22.1) WILD-TYPE                             13
D29V10, multiclass
                                clus
vv                               DEL PEAK  5(2Q22.1) MUTATED
  COLON ADENOCARCINOMA                                    21
  COLON MUCINOUS ADENOCARCINOMA                            3
  RECTAL ADENOCARCINOMA                                   10
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               DEL PEAK  5(2Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     361
  COLON MUCINOUS ADENOCARCINOMA                             59
  RECTAL ADENOCARCINOMA                                    136
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(2Q22.1) MUTATED    25   0   2   2
  DEL PEAK  5(2Q22.1) WILD-TYPE 421   6  35  27
D29V11, multiclass
    clus
vv   DEL PEAK  5(2Q22.1) MUTATED DEL PEAK  5(2Q22.1) WILD-TYPE
  R0                          25                           421
  R1                           0                             6
  R2                           2                            35
  RX                           2                            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"
D29V12, continuous
D29V13, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q22.1) MUTATED     0  16
  DEL PEAK  5(2Q22.1) WILD-TYPE   5 336
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q22.1) MUTATED      0   16
  DEL PEAK  5(2Q22.1) WILD-TYPE    5  336
                        clus
vv                       DEL PEAK  5(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          16
                        clus
vv                       DEL PEAK  5(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           336
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  6(3P26.3) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P26.3) MUTATED    70  21
  DEL PEAK  6(3P26.3) WILD-TYPE 396 107
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           91                           503 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                           21                           107 
$`DEL PEAK  6(3P26.3) MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       14.53         6.05        85.05        31.07        29.98        12.99 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-BM-6198 TCGA-G5-6233 TCGA-5M-AAT4 
        2.01        50.99        24.00        21.24        18.28         1.61 
TCGA-A6-2675 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5667 
       43.43        16.57        34.65        36.53        32.45        29.16 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 
       22.52        25.08        21.76         9.63         5.03         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3855 
       38.99         9.07        29.00        15.02        10.06        32.05 
TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 TCGA-AA-A004 
       17.03         2.01         2.01        21.99         7.96        13.94 
TCGA-AA-A00O TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A02H TCGA-AD-A5EK TCGA-AY-6196 
       27.02        32.02        31.00         2.01        16.44         0.20 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6716 
        5.65         5.13        12.10         3.19        12.59        12.20 
TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
        2.01         8.02        13.02        29.06        22.03         5.03 
TCGA-CM-6163 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 
       14.04        11.08        11.01        20.19        17.75        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA 
       43.27        15.12        17.85        13.41        11.38         7.50 
TCGA-F4-6460 TCGA-NH-A6GA TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2692 
       31.96         9.93        42.77        38.70        11.90        13.55 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3727 TCGA-AG-3731 
       34.49        29.98        20.05        24.00         0.99        37.02 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-4021 TCGA-AG-A02N TCGA-AH-6544 
       19.04        19.99        17.95         3.98        61.97        38.56 
TCGA-CI-6619 TCGA-CI-6624 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6512 TCGA-EI-6514 
        6.05        48.20        25.05        12.62        17.69        16.31 
TCGA-F5-6810 
        0.39 

$`DEL PEAK  6(3P26.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       14.93        24.03        24.00        26.01        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       13.94        19.99        17.03        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       36.03        31.00        51.98        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
        4.80        12.66         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 
       43.76        42.90        42.28        44.91        35.11        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.25        37.02        32.75        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 
       27.09        24.13         8.38        25.18        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        56.25         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 
       37.05        35.01        63.98         1.02         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       21.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.05        47.01        11.01         5.98        37.05         5.03 
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-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       31.07        53.00        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       33.01        26.01        20.98        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D 
       34.06        25.02        27.02        27.02        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q 
       30.02        34.03        18.05        18.05         4.01        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-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        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-A029 
        1.02        33.04         1.02        26.01        37.02        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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
        5.79        22.42        27.42        26.47         0.46         0.92 
TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       14.50        27.09        16.31         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
       58.39         1.41        32.94        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 
       88.21        49.41         6.77        29.56         5.23        11.74 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       12.69        12.36        12.46        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14        82.95       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        25.02        26.04        27.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 
       22.98        30.08        32.02        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-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-6679 TCGA-CM-6680 TCGA-D5-5537 
       12.95        13.05        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.42        18.25 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.35        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        10.98        19.33        19.33        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       16.80        29.46        32.98         8.42        31.30        21.90 
TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       60.13        70.03        46.92        39.48        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.97        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
        7.07        36.03         1.02        46.03        34.03        34.03 
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-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3732 
       15.95        19.99        20.98         7.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       14.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       28.04        36.03        14.04         1.02        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02        49.97         1.94        38.96        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
        2.50        43.20        27.55        26.43        19.46        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        47.44        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA 
       51.98        10.98        44.02        25.97        25.05       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 
        3.48         4.18        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        16.34        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-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        42.35        28.57        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                        85.05                        148.01 
  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE 
                        17.03                         23.87 
[1] "0.2 - 85.0 (17.0)"  "0.0 - 148.0 (23.9)"
[1] "hr=" "1.6"
D30V2, continuous
D30V3, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    70  20
  DEL PEAK  6(3P26.3) WILD-TYPE 378 142
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     70   20
  DEL PEAK  6(3P26.3) WILD-TYPE  378  142
        clus
vv       DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  COLON                           70                           378
  RECTUM                          20                           142
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  6(3P26.3) MUTATED         8        0        4        24         0
  DEL PEAK  6(3P26.3) WILD-TYPE      96        1       33       148        12
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  6(3P26.3) MUTATED           0         4          2         13
  DEL PEAK  6(3P26.3) WILD-TYPE         2        20         13         71
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  6(3P26.3) MUTATED            8       20         5         0
  DEL PEAK  6(3P26.3) WILD-TYPE         47       43        19         2
D30V4, multiclass
            clus
vv           DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  STAGE I                              8                            96
  STAGE IA                             0                             1
  STAGE II                             4                            33
  STAGE IIA                           24                           148
  STAGE IIB                            0                            12
  STAGE IIC                            0                             2
  STAGE III                            4                            20
  STAGE IIIA                           2                            13
  STAGE IIIB                          13                            71
  STAGE IIIC                           8                            47
  STAGE IV                            20                            43
  STAGE IVA                            5                            19
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  6(3P26.3) MUTATED     2   8  70  11
  DEL PEAK  6(3P26.3) WILD-TYPE  18  97 347  58
D30V5, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  T1                           2                            18
  T2                           8                            97
  T3                          70                           347
  T4                          11                            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  6(3P26.3) MUTATED    39  28  24
  DEL PEAK  6(3P26.3) WILD-TYPE 307 122  91
D30V6, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  N0                          39                           307
  N1                          28                           122
  N2                          24                            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"
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    55  25
  DEL PEAK  6(3P26.3) WILD-TYPE 398  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     55   25
  DEL PEAK  6(3P26.3) WILD-TYPE  398   63
   clus
vv  DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  0                          55                           398
  1                          25                            63
[1] 2 2
[1] FALSE
D30V8, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    40  52
  DEL PEAK  6(3P26.3) WILD-TYPE 249 273
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     40   52
  DEL PEAK  6(3P26.3) WILD-TYPE  249  273
        clus
vv       DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  FEMALE                          40                           249
  MALE                            52                           273
[1] 2 2
[1] FALSE
D30V9, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED    76   3
  DEL PEAK  6(3P26.3) WILD-TYPE 406  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED     76    3
  DEL PEAK  6(3P26.3) WILD-TYPE  406   26
     clus
vv    DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  NO                           76                           406
  YES                           3                            26
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                     66
  DEL PEAK  6(3P26.3) WILD-TYPE                  316
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                               4
  DEL PEAK  6(3P26.3) WILD-TYPE                            58
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                      16
  DEL PEAK  6(3P26.3) WILD-TYPE                   130
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  6(3P26.3) MUTATED                                3
  DEL PEAK  6(3P26.3) WILD-TYPE                             10
D30V10, multiclass
                                clus
vv                               DEL PEAK  6(3P26.3) MUTATED
  COLON ADENOCARCINOMA                                    66
  COLON MUCINOUS ADENOCARCINOMA                            4
  RECTAL ADENOCARCINOMA                                   16
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK  6(3P26.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     316
  COLON MUCINOUS ADENOCARCINOMA                             58
  RECTAL ADENOCARCINOMA                                    130
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  6(3P26.3) MUTATED    63   0  11   5
  DEL PEAK  6(3P26.3) WILD-TYPE 383   6  26  24
D30V11, multiclass
    clus
vv   DEL PEAK  6(3P26.3) MUTATED DEL PEAK  6(3P26.3) WILD-TYPE
  R0                          63                           383
  R1                           0                             6
  R2                          11                            26
  RX                           5                            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"
D30V12, continuous
D30V13, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P26.3) MUTATED     2  53
  DEL PEAK  6(3P26.3) WILD-TYPE   3 299
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P26.3) MUTATED      2   53
  DEL PEAK  6(3P26.3) WILD-TYPE    3  299
                        clus
vv                       DEL PEAK  6(3P26.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          53
                        clus
vv                       DEL PEAK  6(3P26.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           299
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  7(3P14.2) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P14.2) MUTATED    90  25
  DEL PEAK  7(3P14.2) WILD-TYPE 376 103
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          115                           479 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                           25                           103 
$`DEL PEAK  7(3P14.2) MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3939 
       14.53         6.05         0.92        85.05        31.07        12.99 
TCGA-AA-3979 TCGA-AA-A00L TCGA-AD-6548 TCGA-AG-3580 TCGA-AG-4008 TCGA-BM-6198 
       24.00        38.04        21.37         8.02        17.03        21.24 
TCGA-G5-6233 TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3807 
       18.28        12.66         1.61        16.57        37.02        34.65 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6651 
       36.53        32.45        29.16        22.52        25.08        21.76 
TCGA-A6-6780 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3517 TCGA-AA-3518 
       20.12        56.25         9.63         5.03        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3664 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3855 
        9.07        54.02        11.01        37.05        10.06        32.05 
TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-3989 
       17.03         2.01         2.01        21.99        27.02         7.96 
TCGA-AA-A004 TCGA-AA-A00J TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A01F TCGA-AA-A01K 
       13.94        18.05        27.02         0.99        32.02        31.00 
TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       41.00        24.53         5.79        16.44         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       109.28         5.65        12.10        12.59 
TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6171 
       12.20         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        25.48 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 TCGA-DM-A1DA 
       43.27        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-NH-A8F8 
       35.97       117.07        31.96        36.00         9.93        16.80 
TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2693 
       42.77        38.70        11.90        70.03        43.04        37.97 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3583 
       34.49        29.98        86.63        11.84         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3592 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 
       24.00        34.03        37.02        32.98        19.04        19.99 
TCGA-AG-3885 TCGA-AG-4007 TCGA-AG-A00C TCGA-AG-A02G TCGA-AH-6544 TCGA-CI-6619 
       17.95         1.02         6.02        38.96        38.56         6.05 
TCGA-CI-6623 TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6508 
       47.44        26.04        10.98        25.05        12.62        20.91 
TCGA-F5-6810 
        0.39 

$`DEL PEAK  7(3P14.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.99        19.00        36.00        19.04        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        24.00         2.01        50.99        26.01 
TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       19.07        21.99        39.06        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 
       26.17        91.79        79.69        17.85        10.39        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       19.99        17.03        25.97        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT6 
       51.98        55.76        26.43        15.62         4.80         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3809 
       42.28        44.91        35.11        37.05        37.25        32.75 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       32.91        31.63        30.44        29.19        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.09        22.06        32.71        27.09        24.13         8.38 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
       25.18        20.61        24.69        24.39        23.87        19.66 
TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-AA-3489 TCGA-AA-3492 
       20.28        16.24        24.92        61.84         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08         6.97         2.01        14.01 
TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 
       50.04        47.05        47.01        15.02         5.98         5.03 
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-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 
       10.06         0.00        33.07         0.00        36.03         0.99 
TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
       31.07        53.00        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       33.01        26.01        20.98        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       34.06        25.02        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       34.03        18.05         4.01        42.02        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        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         1.02 
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-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-6889 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 
       12.16        83.24        22.42        27.42        26.47         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09         0.95        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       17.85        19.33        18.84        58.39         1.41        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.13        22.36        65.00        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
        6.77        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.46        12.39        12.59        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14        82.95       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        25.02        26.04        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        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 
       15.02        15.02        17.03        15.02        12.00        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-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.01        12.95        11.08        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 
       54.61        19.59        56.09        55.92        20.42        18.25 
TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       15.12         4.80        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-A0XD 
        9.44        11.64        13.35        12.00        10.26        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       38.20       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28K 
       14.04        26.47        81.37       119.93        60.79        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       95.18         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       47.87         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 
       55.04        85.48        39.42        61.91        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       19.33        15.65        12.79        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       31.30        21.90        60.13        46.92        39.48        17.23 
TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       13.55        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3586 
       65.98        36.03        12.00        32.02        36.03         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.99        29.98         0.99         0.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 
       32.02        19.99        28.04        36.03        14.04         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        20.98        13.94        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
        1.02         1.02        49.97         1.94        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       33.17        13.78        44.78        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       21.01        25.05        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       51.98        44.02        25.97        25.05       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         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        4.18        20.55        19.96        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-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        42.35        28.57        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                       119.70                        148.01 
  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE 
                        18.28                         23.05 
[1] "0.2 - 119.7 (18.3)" "0.0 - 148.0 (23.1)"
[1] "hr=" "1.2"
D31V2, continuous
D31V3, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    87  29
  DEL PEAK  7(3P14.2) WILD-TYPE 361 133
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     87   29
  DEL PEAK  7(3P14.2) WILD-TYPE  361  133
        clus
vv       DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  COLON                           87                           361
  RECTUM                          29                           133
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  7(3P14.2) MUTATED        19        0        4        32         0
  DEL PEAK  7(3P14.2) WILD-TYPE      85        1       33       140        12
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  7(3P14.2) MUTATED           0         4          1         17
  DEL PEAK  7(3P14.2) WILD-TYPE         2        20         14         67
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  7(3P14.2) MUTATED           11       18         6         1
  DEL PEAK  7(3P14.2) WILD-TYPE         44       45        18         1
D31V4, multiclass
            clus
vv           DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  STAGE I                             19                            85
  STAGE IA                             0                             1
  STAGE II                             4                            33
  STAGE IIA                           32                           140
  STAGE IIB                            0                            12
  STAGE IIC                            0                             2
  STAGE III                            4                            20
  STAGE IIIA                           1                            14
  STAGE IIIB                          17                            67
  STAGE IIIC                          11                            44
  STAGE IV                            18                            45
  STAGE IVA                            6                            18
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  7(3P14.2) MUTATED     7  15  79  16
  DEL PEAK  7(3P14.2) WILD-TYPE  13  90 338  53
D31V5, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  T1                           7                            13
  T2                          15                            90
  T3                          79                           338
  T4                          16                            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  7(3P14.2) MUTATED    59  31  27
  DEL PEAK  7(3P14.2) WILD-TYPE 287 119  88
D31V6, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  N0                          59                           287
  N1                          31                           119
  N2                          27                            88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    76  25
  DEL PEAK  7(3P14.2) WILD-TYPE 377  63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     76   25
  DEL PEAK  7(3P14.2) WILD-TYPE  377   63
   clus
vv  DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  0                          76                           377
  1                          25                            63
[1] 2 2
[1] FALSE
D31V8, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    51  67
  DEL PEAK  7(3P14.2) WILD-TYPE 238 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     51   67
  DEL PEAK  7(3P14.2) WILD-TYPE  238  258
        clus
vv       DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  FEMALE                          51                           238
  MALE                            67                           258
[1] 2 2
[1] FALSE
D31V9, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED    96   5
  DEL PEAK  7(3P14.2) WILD-TYPE 386  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED     96    5
  DEL PEAK  7(3P14.2) WILD-TYPE  386   24
     clus
vv    DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  NO                           96                           386
  YES                           5                            24
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  7(3P14.2) MUTATED                     78
  DEL PEAK  7(3P14.2) WILD-TYPE                  304
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  7(3P14.2) MUTATED                               9
  DEL PEAK  7(3P14.2) WILD-TYPE                            53
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  7(3P14.2) MUTATED                      25
  DEL PEAK  7(3P14.2) WILD-TYPE                   121
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  7(3P14.2) MUTATED                                3
  DEL PEAK  7(3P14.2) WILD-TYPE                             10
D31V10, multiclass
                                clus
vv                               DEL PEAK  7(3P14.2) MUTATED
  COLON ADENOCARCINOMA                                    78
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   25
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK  7(3P14.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     304
  COLON MUCINOUS ADENOCARCINOMA                             53
  RECTAL ADENOCARCINOMA                                    121
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  7(3P14.2) MUTATED    82   1  11   5
  DEL PEAK  7(3P14.2) WILD-TYPE 364   5  26  24
D31V11, multiclass
    clus
vv   DEL PEAK  7(3P14.2) MUTATED DEL PEAK  7(3P14.2) WILD-TYPE
  R0                          82                           364
  R1                           1                             5
  R2                          11                            26
  RX                           5                            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"
D31V12, continuous
D31V13, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P14.2) MUTATED     1  68
  DEL PEAK  7(3P14.2) WILD-TYPE   4 284
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P14.2) MUTATED      1   68
  DEL PEAK  7(3P14.2) WILD-TYPE    4  284
                        clus
vv                       DEL PEAK  7(3P14.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          68
                        clus
vv                       DEL PEAK  7(3P14.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           284
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  8(3Q26.31) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  8(3Q26.31) MUTATED    51  13
  DEL PEAK  8(3Q26.31) WILD-TYPE 415 115
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            64                            530 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                            13                            115 
$`DEL PEAK  8(3Q26.31) MUTATED`
TCGA-A6-4105 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3939 TCGA-AD-6548 TCGA-AG-A014 
       14.53         6.05        85.05        12.99        21.37        15.95 
TCGA-G5-6233 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-AA-3517 
       18.28        16.57        37.25        34.65        32.45        38.99 
TCGA-AA-3529 TCGA-AA-3811 TCGA-AA-3855 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3989 
        0.00        10.06        32.05         2.01        21.99         7.96 
TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A01F TCGA-AA-A01T TCGA-AD-6899 TCGA-AD-A5EK 
       13.94        27.02        32.02        33.04         5.79        16.44 
TCGA-AY-5543 TCGA-AZ-6600 TCGA-CA-6716 TCGA-CM-4752 TCGA-CM-5861 TCGA-CM-5862 
       33.01        12.10        12.20        13.02        15.02         5.03 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6534 
       11.08        11.01        56.09        20.19        25.48        43.27 
TCGA-D5-6536 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28F 
       17.85        13.41        11.38         7.50       131.51        35.97 
TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A6GB TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H 
       82.39        36.00        15.65        42.77        38.70        11.90 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3731 TCGA-AG-4001 
       34.49        29.98        32.02        20.05        37.02        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A02G TCGA-CI-6619 TCGA-DC-6682 TCGA-DT-5265 
       14.04         1.02        38.96         6.05        25.05        12.62 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-7002 
       19.96        20.91         8.61        11.97 

$`DEL PEAK  8(3Q26.31) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       39.06        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       79.69        17.85        10.39         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        25.97        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       21.24        55.76        26.43        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 
       43.43        42.90        42.28        44.91        35.11        37.05 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       37.02        32.75        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        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-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
       37.05        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
        9.07        19.07        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-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-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
        5.98        37.05         5.03        26.99        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 
       37.02         0.00        17.03        10.06         0.00        33.07 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 
        0.00        36.03         0.99        31.07        53.00        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        20.98        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       25.02        27.02        27.02        38.04        19.00        30.02 
TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05         4.01        42.02         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        10.98 
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-A029 TCGA-AA-A02E 
        1.02         1.02        26.01        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W 
       39.98         2.01         5.03         0.92        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       22.42        27.42        26.47         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       27.09        16.31         0.95         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.26        17.85        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
        1.41         5.65        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6603 TCGA-AZ-6605 
       62.79        88.21        49.41         6.77        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         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        25.02        26.04         8.02        27.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5863 TCGA-CM-5864 
       22.03        22.98        30.08        32.02        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 
       45.40        54.61        19.59        55.92        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         4.80        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        13.35        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-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       13.32        12.59       140.38        44.32       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G 
      139.17        14.04        26.47        81.37       119.93        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        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       35.31       133.18         8.35        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 
       10.98        19.33        19.33         9.93        12.79        16.80 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        21.90        60.13 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.97        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       86.63        65.98        11.84        36.03        12.00         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        24.00         1.02        46.03        34.03        34.03 
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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4021 
       48.03        25.02        32.02        19.99        28.04         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
        9.07         1.02         1.02        49.97         1.94        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       26.43        19.46        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       44.02        25.97        25.05       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         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.55        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-6917 
       16.31        16.41        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                             0                              0 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                        131.51                         148.01 
  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE 
                         19.12                          22.39 
[1] "0.0 - 131.5 (19.1)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.1"
D32V2, continuous
D32V3, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    46  17
  DEL PEAK  8(3Q26.31) WILD-TYPE 402 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     46   17
  DEL PEAK  8(3Q26.31) WILD-TYPE  402  145
        clus
vv       DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  COLON                            46                            402
  RECTUM                           17                            145
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  8(3Q26.31) MUTATED         5        0        2        22         0
  DEL PEAK  8(3Q26.31) WILD-TYPE      99        1       35       150        12
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  8(3Q26.31) MUTATED           0         2          0          5
  DEL PEAK  8(3Q26.31) WILD-TYPE         2        22         15         79
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  8(3Q26.31) MUTATED            9       13         4         0
  DEL PEAK  8(3Q26.31) WILD-TYPE         46       50        20         2
D32V4, multiclass
            clus
vv           DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  STAGE I                               5                             99
  STAGE IA                              0                              1
  STAGE II                              2                             35
  STAGE IIA                            22                            150
  STAGE IIB                             0                             12
  STAGE IIC                             0                              2
  STAGE III                             2                             22
  STAGE IIIA                            0                             15
  STAGE IIIB                            5                             79
  STAGE IIIC                            9                             46
  STAGE IV                             13                             50
  STAGE IVA                             4                             20
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK  8(3Q26.31) MUTATED     0   6  49   9
  DEL PEAK  8(3Q26.31) WILD-TYPE  20  99 368  60
D32V5, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  T1                            0                             20
  T2                            6                             99
  T3                           49                            368
  T4                            9                             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  8(3Q26.31) MUTATED    31  14  19
  DEL PEAK  8(3Q26.31) WILD-TYPE 315 136  96
D32V6, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  N0                           31                            315
  N1                           14                            136
  N2                           19                             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"
D32V7, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    41  16
  DEL PEAK  8(3Q26.31) WILD-TYPE 412  72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     41   16
  DEL PEAK  8(3Q26.31) WILD-TYPE  412   72
   clus
vv  DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  0                           41                            412
  1                           16                             72
[1] 2 2
[1] FALSE
D32V8, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    27  37
  DEL PEAK  8(3Q26.31) WILD-TYPE 262 288
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     27   37
  DEL PEAK  8(3Q26.31) WILD-TYPE  262  288
        clus
vv       DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  FEMALE                           27                            262
  MALE                             37                            288
[1] 2 2
[1] FALSE
D32V9, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED    54   2
  DEL PEAK  8(3Q26.31) WILD-TYPE 428  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED     54    2
  DEL PEAK  8(3Q26.31) WILD-TYPE  428   27
     clus
vv    DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  NO                            54                            428
  YES                            2                             27
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                     43
  DEL PEAK  8(3Q26.31) WILD-TYPE                  339
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                               3
  DEL PEAK  8(3Q26.31) WILD-TYPE                            59
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                      12
  DEL PEAK  8(3Q26.31) WILD-TYPE                   134
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  8(3Q26.31) MUTATED                                5
  DEL PEAK  8(3Q26.31) WILD-TYPE                              8
D32V10, multiclass
                                clus
vv                               DEL PEAK  8(3Q26.31) MUTATED
  COLON ADENOCARCINOMA                                     43
  COLON MUCINOUS ADENOCARCINOMA                             3
  RECTAL ADENOCARCINOMA                                    12
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK  8(3Q26.31) WILD-TYPE
  COLON ADENOCARCINOMA                                      339
  COLON MUCINOUS ADENOCARCINOMA                              59
  RECTAL ADENOCARCINOMA                                     134
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  8(3Q26.31) MUTATED    48   0   6   2
  DEL PEAK  8(3Q26.31) WILD-TYPE 398   6  31  27
D32V11, multiclass
    clus
vv   DEL PEAK  8(3Q26.31) MUTATED DEL PEAK  8(3Q26.31) WILD-TYPE
  R0                           48                            398
  R1                            0                              6
  R2                            6                             31
  RX                            2                             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"
D32V12, continuous
D32V13, binary
                                cls
clus                               0   1
  DEL PEAK  8(3Q26.31) MUTATED     0  41
  DEL PEAK  8(3Q26.31) WILD-TYPE   5 311
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(3Q26.31) MUTATED      0   41
  DEL PEAK  8(3Q26.31) WILD-TYPE    5  311
                        clus
vv                       DEL PEAK  8(3Q26.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       DEL PEAK  8(3Q26.31) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            311
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  9(4P16.1) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4P16.1) MUTATED   149  44
  DEL PEAK  9(4P16.1) WILD-TYPE 317  84
  DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE 
                          193                           401 
  DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE 
                           44                            84 
$`DEL PEAK  9(4P16.1) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3562 
       13.94        14.53        37.05        34.03        13.02        19.99 
TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
        6.05        36.00        85.05        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-CK-5912 TCGA-DM-A285 
       12.99         2.01        50.99        26.01        49.08         5.88 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A00H 
       23.51        63.62        91.79        13.94        17.03        25.97 
TCGA-BM-6198 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       21.24        26.43         4.80         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2686 
       43.76        44.91        35.11        16.57        37.05        37.02 
TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5667 TCGA-A6-6648 TCGA-A6-6651 
       36.53        32.45        30.44        29.16        25.18        21.76 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3517 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3664 TCGA-AA-3666 
        7.04        38.99        12.99        21.01        54.02         2.01 
TCGA-AA-3673 TCGA-AA-3679 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       50.04        15.02        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       10.06        33.07        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F 
       17.03         2.01        20.98         2.01        21.99        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-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 
        2.96        39.98         2.01        41.00         5.79        22.42 
TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
       26.47        14.50         0.95        33.01         0.20        17.85 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5256 
        5.13        65.00        12.10        29.56         3.19        12.46 
TCGA-CA-5797 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5864 
       12.59         8.02        29.06        22.03        22.98        15.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6677 
       17.03        14.04        29.03        13.02        15.02        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 
       11.01        10.06        45.40        56.09        20.19        17.75 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 
       12.43        14.30         9.04        13.41        11.38        12.59 
TCGA-DM-A1DA TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 
        7.50        14.04        26.47         1.55        43.04        33.67 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U 
       47.41         8.35        61.91        46.75        18.18        10.98 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-SS-A7HO TCGA-T9-A92H 
       16.80        42.77        29.46        21.90        60.13        11.90 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       46.92        17.23        43.04        34.49        37.74        29.98 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 
       24.36        24.59        65.98        36.03        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 
       34.03        34.03         6.05        20.98        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       32.98        19.04         1.02        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 
       32.02        19.99        28.04        36.03        14.04        13.94 
TCGA-AG-A00Y TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 
       23.01        38.96        41.00        43.20         6.05        33.17 
TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       48.20        31.00        31.00        51.98        10.98        44.02 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 
      126.44       129.27        32.61         4.18        15.85        16.34 
TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       16.41        11.97         8.45        42.35        28.57         0.39 
TCGA-F5-6813 
       19.66 

$`DEL PEAK  9(4P16.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        45.60        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3554 
       24.03        36.03         8.05        19.07         0.99        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 
       23.01        19.99         0.92        19.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3950 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       14.93        24.00        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6314 TCGA-G4-6321 
      106.75       100.01         1.94        28.21        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       35.80        26.17        79.69        17.85        10.39         8.02 
TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       19.99        17.03        15.95        36.03        31.00        51.98 
TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 
       18.28        55.76        15.62        12.66         9.53        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 
       43.43        42.90        42.28        37.25        34.65        32.75 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       32.91        31.63        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-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.08        20.61        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
       16.24        24.92         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         6.97         1.02         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        26.01        14.01        33.99 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3681 
        6.97        14.01        47.05        47.01        11.01         5.98 
TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       37.05         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 
       25.02         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
        0.00        36.03        27.02        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       33.01        26.01        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        18.05        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
        0.99        17.03        14.99        34.98        15.02        10.98 
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-A029 TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
        1.02        37.02        51.98         5.03         0.92        22.03 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 
       27.42        16.44         0.46         0.92        27.09        16.31 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.65        32.94        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
       88.21        49.41         6.77         5.23        11.74        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.39        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         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        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 
       13.02        30.08        32.02        15.02         5.03        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       15.02        12.00        16.04        21.99        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6680 
       14.04        11.01        12.95        13.05        11.08        12.03 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       54.61        19.59        55.92        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       43.27        15.12        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6927 
       16.14        15.58         7.53        12.39        10.13         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.35        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28C 
       44.32       131.51       135.65         7.76       139.17        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        31.96        11.11        35.74        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 
       47.87        34.42        41.42        13.25         0.53        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       26.04        13.78        74.79        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL 
       15.65        12.79        32.98         8.42        31.30        38.70 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6655 
       70.03        39.48        13.55        37.97        16.83        20.02 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       20.05        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-3742 
        0.99        15.95        19.99         7.99         0.99         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        0.99        19.99        17.95        36.95        13.02        14.01 
TCGA-AG-3901 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       25.02         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       61.97        38.04        38.56         2.50        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       19.46        13.78        44.78        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 
       21.01        25.05        26.04        12.00        13.97        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        25.05        12.62        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48         3.48        20.55        19.96        20.91        17.00 
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-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 
       13.64        17.46         9.96        49.51        32.19        36.49 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE 
                       129.27                        148.01 
  DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE 
                        24.36                         20.98 
[1] "0.2 - 129.3 (24.4)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.2"
D33V2, continuous
D33V3, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.1) MUTATED   137  62
  DEL PEAK  9(4P16.1) WILD-TYPE 311 100
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.1) MUTATED    137   62
  DEL PEAK  9(4P16.1) WILD-TYPE  311  100
        clus
vv       DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE
  COLON                          137                           311
  RECTUM                          62                           100
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK  9(4P16.1) MUTATED        29        0        8        49         3
  DEL PEAK  9(4P16.1) WILD-TYPE      75        1       29       123         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK  9(4P16.1) MUTATED           0         5          8         25
  DEL PEAK  9(4P16.1) WILD-TYPE         2        19          7         59
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK  9(4P16.1) MUTATED           25       34        10         0
  DEL PEAK  9(4P16.1) WILD-TYPE         30       29        14         2
D33V4, multiclass
            clus
vv           DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE
  STAGE I                             29                            75
  STAGE IA                             0                             1
  STAGE II                             8                            29
  STAGE IIA                           49                           123
  STAGE IIB                            3                             9
  STAGE IIC                            0                             2
  STAGE III                            5                            19
  STAGE IIIA                           8                             7
  STAGE IIIB                          25                            59
  STAGE IIIC                          25                            30
  STAGE IV                            34                            29
  STAGE IVA                           10                            14
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK  9(4P16.1) MUTATED     6  34 135  25
  DEL PEAK  9(4P16.1) WILD-TYPE  14  71 282  44
D33V5, multiclass
    clus
vv   DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE
  T1                           6                            14
  T2                          34                            71
  T3                         135                           282
  T4                          25                            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  9(4P16.1) MUTATED    93  56  51
  DEL PEAK  9(4P16.1) WILD-TYPE 253  94  64
D33V6, multiclass
    clus
vv   DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE
  N0                          93                           253
  N1                          56                            94
  N2                          51                            64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.1) MUTATED   133  42
  DEL PEAK  9(4P16.1) WILD-TYPE 320  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.1) MUTATED    133   42
  DEL PEAK  9(4P16.1) WILD-TYPE  320   46
   clus
vv  DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE
  0                         133                           320
  1                          42                            46
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.1) MUTATED    84 117
  DEL PEAK  9(4P16.1) WILD-TYPE 205 208
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.1) MUTATED     84  117
  DEL PEAK  9(4P16.1) WILD-TYPE  205  208
        clus
vv       DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE
  FEMALE                          84                           205
  MALE                           117                           208
[1] 2 2
[1] FALSE
D33V9, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.1) MUTATED   154  15
  DEL PEAK  9(4P16.1) WILD-TYPE 328  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.1) MUTATED    154   15
  DEL PEAK  9(4P16.1) WILD-TYPE  328   14
     clus
vv    DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE
  NO                          154                           328
  YES                          15                            14
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK  9(4P16.1) MUTATED                    126
  DEL PEAK  9(4P16.1) WILD-TYPE                  256
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4P16.1) MUTATED                              11
  DEL PEAK  9(4P16.1) WILD-TYPE                            51
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK  9(4P16.1) MUTATED                      57
  DEL PEAK  9(4P16.1) WILD-TYPE                    89
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK  9(4P16.1) MUTATED                                4
  DEL PEAK  9(4P16.1) WILD-TYPE                              9
D33V10, multiclass
                                clus
vv                               DEL PEAK  9(4P16.1) MUTATED
  COLON ADENOCARCINOMA                                   126
  COLON MUCINOUS ADENOCARCINOMA                           11
  RECTAL ADENOCARCINOMA                                   57
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK  9(4P16.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     256
  COLON MUCINOUS ADENOCARCINOMA                             51
  RECTAL ADENOCARCINOMA                                     89
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  9(4P16.1) MUTATED   147   1  16   6
  DEL PEAK  9(4P16.1) WILD-TYPE 299   5  21  23
D33V11, multiclass
    clus
vv   DEL PEAK  9(4P16.1) MUTATED DEL PEAK  9(4P16.1) WILD-TYPE
  R0                         147                           299
  R1                           1                             5
  R2                          16                            21
  RX                           6                            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"
D33V12, continuous
D33V13, binary
                               cls
clus                              0   1
  DEL PEAK  9(4P16.1) MUTATED     3 108
  DEL PEAK  9(4P16.1) WILD-TYPE   2 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4P16.1) MUTATED      3  108
  DEL PEAK  9(4P16.1) WILD-TYPE    2  244
                        clus
vv                       DEL PEAK  9(4P16.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         108
                        clus
vv                       DEL PEAK  9(4P16.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           244
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK 10(4Q22.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 10(4Q22.1) MUTATED   166  49
  DEL PEAK 10(4Q22.1) WILD-TYPE 300  79
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                          215                           379 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                           49                            79 
$`DEL PEAK 10(4Q22.1) MUTATED`
TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3562 
       13.94        24.16        37.05        34.03        13.02        19.99 
TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3860 TCGA-AA-3952 TCGA-AA-3972 
        6.05        36.00        19.04        31.07         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       26.01        24.00       106.75        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 
       23.51        63.62        91.79        13.94        19.99        17.03 
TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 
       25.97        21.24        18.28        26.43         4.80         1.61 
TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       39.45        43.76        43.43        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 
       37.05        34.65        36.53        32.45        29.19        29.16 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       20.61        21.76        23.87        20.28        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3517 
        9.63         5.03         7.04        63.98         6.97        38.99 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 
        0.00        29.00        33.99        21.01         2.01        50.04 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       37.05        10.06        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3930 TCGA-AA-3955 
       10.06        33.07         0.99        17.03         2.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00Q 
       34.03         2.01        21.99        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         5.79        22.42        26.47        14.50        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4616 TCGA-AZ-4684 
        0.95         0.20        17.85        18.84         5.13        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-4948 
       12.10        29.56        12.46        12.59        14.30       148.01 
TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 
       20.02         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        45.40        56.09 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6924 
       20.19        17.75        25.48        43.27        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-A288 TCGA-DM-A28F TCGA-F4-6460 TCGA-F4-6807 
        7.50        44.32        14.04        35.97        31.96        43.04 
TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 TCGA-G4-6626 
       33.67        47.41         8.35        82.39        61.91        46.75 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       18.18        10.98         9.93        16.80        42.77        29.46 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2690 
       21.90        38.70        60.13        11.90        46.92        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 
       24.36        65.98        36.03        34.03        34.03         6.05 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 
       20.98        29.98        32.98        19.04         1.02        17.95 
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-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02X 
        1.02        13.94         6.02        23.01         1.94        41.00 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6624 
       38.56        43.20         6.05        33.17        13.78        48.20 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       25.05        31.00        31.00        51.98        10.98        44.02 
TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 
       25.05       126.44       129.27         4.18        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       15.85        16.34        16.41        11.97         8.45        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       28.57         0.39        32.19        36.49        19.66 

$`DEL PEAK 10(4Q22.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        45.60        14.53         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3554 
       24.03        36.03         8.05        19.07         0.99        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 
       23.01        19.99         0.92        19.00        85.05        19.04 
TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3986 
       14.93        24.03        29.98        12.99        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6314 TCGA-G4-6321 
       10.88        75.95       100.01         1.94        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       35.80        26.17        79.69        17.85        10.39         8.02 
TCGA-AG-3890 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
       17.03        15.95        36.03        31.00        51.98        55.76 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 
       15.62        12.66         9.53        43.76        46.65        42.90 
TCGA-A6-2678 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5656 TCGA-A6-5657 
       42.28        37.25        37.02        32.75        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-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       27.09        22.52        24.13         8.38        25.08        25.18 
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-3502 TCGA-AA-3514 TCGA-AA-3518 
        3.02         1.02        37.05        35.01         1.02         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        9.07        19.07        29.00        26.01        12.99        14.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
        6.97        54.02        14.01        47.05        47.01        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.98         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 
       25.02         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 
        0.00        36.03        32.05        31.07        53.00        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3971 
       18.05        31.00        24.00        33.01        26.01        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       27.02         0.99        14.99        34.98        15.02        10.98 
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-A01Z TCGA-AA-A029 TCGA-AA-A02H 
        1.02        33.04         1.02        37.02        51.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       12.16        83.24        24.53        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
        0.92        27.09        33.01        21.44        17.82        17.26 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 
       22.36        62.79        88.21        49.41         6.77         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.20        12.76        10.06        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 
      124.27        23.05        37.02        25.02        26.04        27.02 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 
       22.98        30.08        32.02        15.02        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-6674 TCGA-CM-6676 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 
       12.95        11.08        10.06        12.03        54.61        19.59 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       55.92        20.42        18.25        17.85         4.80        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-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 TCGA-DM-A0X9 
       12.43         9.44        11.64        13.35        10.26       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       140.38 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
      131.51       135.65         7.76       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
      119.93        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        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 
       34.42        41.42        13.25         0.53        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       85.48        39.42        36.00        26.43        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YX 
       74.79        19.33        19.33        15.65        12.79        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6655 
        8.42        31.30        70.03        39.48        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.59        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        7.07        20.05        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-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        7.99         0.99        37.02         0.99         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 
       36.95        13.02        35.01        14.01        25.02        32.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
        3.98        46.03        20.98        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
        1.02        49.97        38.96        61.97        38.04         2.50 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
       27.55        26.43        19.46        44.78        47.44        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 
        7.17        21.01        26.04        12.00        13.97        25.97 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       25.05        12.62        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 
       32.61         3.48        20.55        19.96        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        9.96        49.51        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                            0                             0 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                       148.01                        140.38 
  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE 
                        22.03                         21.99 
[1] "0.0 - 148.0 (22.0)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.2"
D34V2, continuous
D34V3, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   149  70
  DEL PEAK 10(4Q22.1) WILD-TYPE 299  92
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    149   70
  DEL PEAK 10(4Q22.1) WILD-TYPE  299   92
        clus
vv       DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  COLON                          149                           299
  RECTUM                          70                            92
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 10(4Q22.1) MUTATED        26        0       11        59         3
  DEL PEAK 10(4Q22.1) WILD-TYPE      78        1       26       113         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 10(4Q22.1) MUTATED           0         5          7         37
  DEL PEAK 10(4Q22.1) WILD-TYPE         2        19          8         47
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 10(4Q22.1) MUTATED           29       27        10         1
  DEL PEAK 10(4Q22.1) WILD-TYPE         26       36        14         1
D34V4, multiclass
            clus
vv           DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  STAGE I                             26                            78
  STAGE IA                             0                             1
  STAGE II                            11                            26
  STAGE IIA                           59                           113
  STAGE IIB                            3                             9
  STAGE IIC                            0                             2
  STAGE III                            5                            19
  STAGE IIIA                           7                             8
  STAGE IIIB                          37                            47
  STAGE IIIC                          29                            26
  STAGE IV                            27                            36
  STAGE IVA                           10                            14
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 10(4Q22.1) MUTATED     6  29 158  29
  DEL PEAK 10(4Q22.1) WILD-TYPE  14  76 259  40
D34V5, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  T1                           6                            14
  T2                          29                            76
  T3                         158                           259
  T4                          29                            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 10(4Q22.1) MUTATED   103  65  54
  DEL PEAK 10(4Q22.1) WILD-TYPE 243  85  61
D34V6, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  N0                         103                           243
  N1                          65                            85
  N2                          54                            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"
D34V7, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   155  38
  DEL PEAK 10(4Q22.1) WILD-TYPE 298  50
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    155   38
  DEL PEAK 10(4Q22.1) WILD-TYPE  298   50
   clus
vv  DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  0                         155                           298
  1                          38                            50
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED    95 128
  DEL PEAK 10(4Q22.1) WILD-TYPE 194 197
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED     95  128
  DEL PEAK 10(4Q22.1) WILD-TYPE  194  197
        clus
vv       DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  FEMALE                          95                           194
  MALE                           128                           197
[1] 2 2
[1] FALSE
D34V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED   175  14
  DEL PEAK 10(4Q22.1) WILD-TYPE 307  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED    175   14
  DEL PEAK 10(4Q22.1) WILD-TYPE  307   15
     clus
vv    DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  NO                          175                           307
  YES                          14                            15
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                    138
  DEL PEAK 10(4Q22.1) WILD-TYPE                  244
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                              11
  DEL PEAK 10(4Q22.1) WILD-TYPE                            51
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                      65
  DEL PEAK 10(4Q22.1) WILD-TYPE                    81
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 10(4Q22.1) MUTATED                                4
  DEL PEAK 10(4Q22.1) WILD-TYPE                              9
D34V10, multiclass
                                clus
vv                               DEL PEAK 10(4Q22.1) MUTATED
  COLON ADENOCARCINOMA                                   138
  COLON MUCINOUS ADENOCARCINOMA                           11
  RECTAL ADENOCARCINOMA                                   65
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK 10(4Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     244
  COLON MUCINOUS ADENOCARCINOMA                             51
  RECTAL ADENOCARCINOMA                                     81
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 10(4Q22.1) MUTATED   164   3  12   8
  DEL PEAK 10(4Q22.1) WILD-TYPE 282   3  25  21
D34V11, multiclass
    clus
vv   DEL PEAK 10(4Q22.1) MUTATED DEL PEAK 10(4Q22.1) WILD-TYPE
  R0                         164                           282
  R1                           3                             3
  R2                          12                            25
  RX                           8                            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"
D34V12, continuous
D34V13, binary
                               cls
clus                              0   1
  DEL PEAK 10(4Q22.1) MUTATED     3 131
  DEL PEAK 10(4Q22.1) WILD-TYPE   2 221
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(4Q22.1) MUTATED      3  131
  DEL PEAK 10(4Q22.1) WILD-TYPE    2  221
                        clus
vv                       DEL PEAK 10(4Q22.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         131
                        clus
vv                       DEL PEAK 10(4Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           221
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 11(4Q35.1) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(4Q35.1) MUTATED   174  48
  DEL PEAK 11(4Q35.1) WILD-TYPE 292  80
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          222                           372 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                           48                            80 
$`DEL PEAK 11(4Q35.1) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3522 TCGA-AA-3531 TCGA-AA-3552 
       45.60        13.94        24.16        37.05        34.03        13.02 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3972 
       19.99         6.05        36.00        85.05        31.07        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 
       26.01        24.00        38.04        49.08         5.88        23.51 
TCGA-G4-6310 TCGA-G4-6625 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H 
       63.62        91.79        10.39        13.94        19.99        25.97 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE 
       21.24        18.28        26.43         4.80         1.61        39.45 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       43.76        43.43        35.11        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5660 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 
       34.65        32.45        29.19        29.16        22.52        24.13 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B 
       20.61        21.76        23.87        20.28        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3532 TCGA-AA-3538 
        9.63         5.03         6.97        38.99        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 
       14.01        33.99        21.01        78.08        54.02         2.01 
TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       50.04        37.05        10.06        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3866 
       17.03        10.06        33.07        36.03         0.99        17.03 
TCGA-AA-3930 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-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
        7.96        34.03        42.02        15.02        32.02        31.00 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       35.01         1.02        26.01         2.96        39.98         2.01 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       41.00        22.42        26.47        14.50        16.31         0.95 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 
        0.20        17.85       109.28         5.65         5.13        65.00 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-6718 TCGA-CA-6719 
       12.10        29.56        12.69        12.46        10.06        14.30 
TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
        8.02        13.02        29.06        22.03        22.98        30.08 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 
        5.03        15.02        15.02        17.03        14.04        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 
       13.02        15.02        11.01        11.08        11.01        45.40 
TCGA-D5-5540 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 
       56.09        20.19        17.75        25.48        43.27        17.85 
TCGA-D5-6898 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
        7.53         9.04        13.41        13.32       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 
       44.32       131.51        14.04        26.47        31.96         1.55 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 
       43.04        33.67        47.41         8.35        82.39        61.91 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 
       46.75        18.18        10.98         9.93        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
       42.77        29.46        21.90        38.70        60.13        11.90 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       46.92        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3587 
       37.74        29.98        24.36        65.98        36.03        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3732 
       34.03        34.03         6.05        20.98        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3898 TCGA-AG-3909 
        0.99        19.04         1.02        17.95        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A00Y 
       28.04        36.03        14.04         3.98        13.94        23.01 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       41.00        38.56        43.20         6.05        33.17        13.78 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       48.20        25.05        31.00        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6509 
       44.02       126.44       129.27        24.13         4.18        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        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6864 
       28.57         0.39        32.19        36.49        37.18        12.46 

$`DEL PEAK 11(4Q35.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        14.53         1.02        58.03        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 
       36.03         8.05        19.07         0.99        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.99         0.92        19.00        19.04        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3986 
       24.03        29.98        12.99        24.00         2.01        19.07 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6314 
       75.95       106.75       100.01         1.94        28.21        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 
       22.09        35.80        26.17        79.69        17.85         8.02 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        15.95        36.03        31.00        51.98 
TCGA-G5-6235 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 
       55.76        15.62        12.66         9.53        43.76        46.65 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 
       42.90        42.28        44.91        37.02        32.75        36.53 
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-A6-6137 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       22.06        32.71        27.09         8.38        25.08        25.18 
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-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 
        1.02         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       12.99        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        6.97        14.01        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.98         5.03        26.99        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
        1.02        17.98        15.95         0.00         0.00         0.00 
TCGA-AA-3855 TCGA-AA-3858 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-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       24.00        33.01        26.01        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        27.02        13.94        38.04        19.00        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-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       14.99        34.98        15.02        10.98        12.00        31.00 
TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
       38.07         1.02        33.04         1.02        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK 
       12.16        83.24        24.53         5.79        27.42        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 
        0.46         0.92        27.09        33.01        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 
       17.26        19.33        18.84        58.39         1.41        32.94 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6605 
       22.36        62.79        88.21        49.41         6.77         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74         3.19        12.36        12.39        12.59        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       12.20        12.76        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         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        25.02        26.04 
TCGA-CM-4751 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       27.02        32.02        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-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        54.61        19.59        55.92 
TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       20.42        18.25        15.12         4.80        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        13.35        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        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       41.42        13.25         0.53        35.31       133.18        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 
       39.42        36.00        26.43        26.04        13.78        74.79 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       19.33        19.33        15.65        32.98         8.42        31.30 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       70.03        39.48        16.83        20.02        24.59        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 
       11.84        36.03        12.00        32.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 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-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
        1.02        25.02        32.02         1.02        46.03        20.98 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
        6.02        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
        1.94        38.96        61.97        38.04         2.50        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       26.43        19.46        44.78        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 
       21.01        26.04        12.00        13.97        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
       25.05        12.62        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-6512 
        3.48        20.55        19.96        20.91        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
        8.45        49.51        19.66        38.14        11.87        47.08 

  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                       140.38                        148.01 
  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE 
                       24.065                        20.980 
[1] "0.2 - 140.4 (24.1)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1"  
D35V2, continuous
D35V3, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   158  69
  DEL PEAK 11(4Q35.1) WILD-TYPE 290  93
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    158   69
  DEL PEAK 11(4Q35.1) WILD-TYPE  290   93
        clus
vv       DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  COLON                          158                           290
  RECTUM                          69                            93
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 11(4Q35.1) MUTATED        31        0       10        62         2
  DEL PEAK 11(4Q35.1) WILD-TYPE      73        1       27       110        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 11(4Q35.1) MUTATED           0         7          7         35
  DEL PEAK 11(4Q35.1) WILD-TYPE         2        17          8         49
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 11(4Q35.1) MUTATED           30       30        10         1
  DEL PEAK 11(4Q35.1) WILD-TYPE         25       33        14         1
D35V4, multiclass
            clus
vv           DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  STAGE I                             31                            73
  STAGE IA                             0                             1
  STAGE II                            10                            27
  STAGE IIA                           62                           110
  STAGE IIB                            2                            10
  STAGE IIC                            0                             2
  STAGE III                            7                            17
  STAGE IIIA                           7                             8
  STAGE IIIB                          35                            49
  STAGE IIIC                          30                            25
  STAGE IV                            30                            33
  STAGE IVA                           10                            14
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 11(4Q35.1) MUTATED     7  33 163  27
  DEL PEAK 11(4Q35.1) WILD-TYPE  13  72 254  42
D35V5, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  T1                           7                            13
  T2                          33                            72
  T3                         163                           254
  T4                          27                            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 11(4Q35.1) MUTATED   109  64  57
  DEL PEAK 11(4Q35.1) WILD-TYPE 237  86  58
D35V6, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  N0                         109                           237
  N1                          64                            86
  N2                          57                            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"
D35V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   163  41
  DEL PEAK 11(4Q35.1) WILD-TYPE 290  47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    163   41
  DEL PEAK 11(4Q35.1) WILD-TYPE  290   47
   clus
vv  DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  0                         163                           290
  1                          41                            47
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   108 123
  DEL PEAK 11(4Q35.1) WILD-TYPE 181 202
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    108  123
  DEL PEAK 11(4Q35.1) WILD-TYPE  181  202
        clus
vv       DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  FEMALE                         108                           181
  MALE                           123                           202
[1] 2 2
[1] FALSE
D35V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED   180  15
  DEL PEAK 11(4Q35.1) WILD-TYPE 302  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED    180   15
  DEL PEAK 11(4Q35.1) WILD-TYPE  302   14
     clus
vv    DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  NO                          180                           302
  YES                          15                            14
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                    141
  DEL PEAK 11(4Q35.1) WILD-TYPE                  241
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                              16
  DEL PEAK 11(4Q35.1) WILD-TYPE                            46
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                      65
  DEL PEAK 11(4Q35.1) WILD-TYPE                    81
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 11(4Q35.1) MUTATED                                3
  DEL PEAK 11(4Q35.1) WILD-TYPE                             10
D35V10, multiclass
                                clus
vv                               DEL PEAK 11(4Q35.1) MUTATED
  COLON ADENOCARCINOMA                                   141
  COLON MUCINOUS ADENOCARCINOMA                           16
  RECTAL ADENOCARCINOMA                                   65
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK 11(4Q35.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     241
  COLON MUCINOUS ADENOCARCINOMA                             46
  RECTAL ADENOCARCINOMA                                     81
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 11(4Q35.1) MUTATED   167   2  15   9
  DEL PEAK 11(4Q35.1) WILD-TYPE 279   4  22  20
D35V11, multiclass
    clus
vv   DEL PEAK 11(4Q35.1) MUTATED DEL PEAK 11(4Q35.1) WILD-TYPE
  R0                         167                           279
  R1                           2                             4
  R2                          15                            22
  RX                           9                            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"
D35V12, continuous
D35V13, binary
                               cls
clus                              0   1
  DEL PEAK 11(4Q35.1) MUTATED     3 135
  DEL PEAK 11(4Q35.1) WILD-TYPE   2 217
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(4Q35.1) MUTATED      3  135
  DEL PEAK 11(4Q35.1) WILD-TYPE    2  217
                        clus
vv                       DEL PEAK 11(4Q35.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         135
                        clus
vv                       DEL PEAK 11(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           217
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 12(5Q12.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(5Q12.1) MUTATED   115  38
  DEL PEAK 12(5Q12.1) WILD-TYPE 351  90
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          153                           441 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                           38                            90 
$`DEL PEAK 12(5Q12.1) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3688 
       13.94        14.53        24.16        13.02        19.99        19.00 
TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3952 TCGA-AZ-6608 TCGA-CK-5912 
       85.05        31.07        24.03         2.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6625 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3890 
        5.88        63.62        91.79        10.39        13.94        17.03 
TCGA-AG-4008 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-5M-AAT4 TCGA-5M-AATE 
       17.03        21.24        18.28        26.43         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2683 TCGA-A6-2686 
       43.76        43.76        43.43        42.90        16.57        37.02 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6142 
       34.65        36.53        30.44        29.19        27.09        25.08 
TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 
       25.18        21.76        24.69        23.87         9.63         5.03 
TCGA-AA-3502 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3678 
       35.01        26.01        12.99        24.00        50.04        47.01 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3856 
       37.05        10.06        36.95        37.02        33.07         0.99 
TCGA-AA-3858 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
       31.07         2.01        21.99        34.03        27.02        42.02 
TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6901 
       10.98        33.04         2.96         2.01        41.00        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A54L TCGA-AY-A71X 
       27.42        26.47        16.31         0.20        17.26        19.33 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5797 
        5.65        65.00        62.79        29.56         5.23        12.59 
TCGA-CA-6719 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 
       14.30        25.02         8.02        13.02        29.06        22.03 
TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-D5-6531 
        5.03        15.02        14.04        29.03        13.02        17.75 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-DM-A1DB 
       17.85         7.53        10.13        12.43         9.04        44.32 
TCGA-DM-A1HA TCGA-F4-6459 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 
      131.51         8.61         1.55        33.67         8.35        82.39 
TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 
       36.00        18.18        10.98        12.79        42.77         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 
       21.90        38.70        46.92        17.23        43.04        37.74 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3591 TCGA-AG-3725 TCGA-AG-3728 
       24.36        24.59        86.63        34.03        20.98        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 
       37.02        32.98        19.04        19.99         1.02        48.03 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G 
       28.04        36.03         3.98        23.01         1.94        38.96 
TCGA-AG-A02X TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       41.00        33.17         7.17        31.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE 
       51.98        10.98        25.05       126.44        57.24       129.27 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       51.48        20.55        16.41        13.64        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 
       49.51        28.57        32.19 

$`DEL PEAK 12(5Q12.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60         1.02        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 
       17.95        23.01        19.99         6.05         0.92        36.00 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        19.04        14.93        29.98        12.99        24.00 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 
      106.75       100.01        28.21        23.51        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3612 
       35.80        26.17        79.69        17.85         8.02        19.99 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
       25.97        15.95        36.03        31.00        51.98        55.76 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2678 
       15.62         4.80        12.66         9.53        46.65        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3809 TCGA-A6-4107 
       44.91        35.11        37.05        37.25        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 
       32.71        29.16        22.52        24.13         8.38        20.61 
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-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       61.84        56.25         7.04         3.02         1.02        37.05 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 
       19.07         0.00        29.00        29.00        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3679 
        6.97        54.02         2.01        14.01        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.98         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        38.99         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       17.03        10.06         0.00         0.00        36.03        32.05 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         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-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
        4.01         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z 
        1.02        35.01         1.02         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       51.98        39.98         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       16.44         0.46         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
       33.01        21.44        17.82        17.85        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41        32.94         5.13        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       49.41         6.77        12.10        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         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        32.02        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        45.40        54.61        19.59 
TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       56.09        55.92        20.19        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        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 
       13.35        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        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
        6.18        47.87        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 
        0.53        47.41        35.31       133.18        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       61.91        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33        19.33         9.93        15.65        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 
       32.98        31.30        60.13        11.90        70.03        39.48 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       13.55        37.97        34.49        29.98        16.83        20.02 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        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-3592 
       36.03        20.05        24.00         1.02        46.03        34.03 
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-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 
       15.95        19.99         7.99         0.99         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       25.02        32.02        19.99        14.04         1.02        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        13.94         6.02        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.02        49.97        61.97        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6621 
       43.20        27.55        26.43        19.46         6.05        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
       44.78        47.44        48.20        78.12        21.01        25.05 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       26.04        12.00        44.02        25.97        25.05        12.62 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       41.36        24.13        32.61         3.48         4.18        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 
       42.35         0.39        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                       131.51                        148.01 
  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE 
                        24.16                         21.01 
[1] "0.2 - 131.5 (24.2)" "0.0 - 148.0 (21.0)"
[1] "hr=" "1.3"
D36V2, continuous
D36V3, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED   105  53
  DEL PEAK 12(5Q12.1) WILD-TYPE 343 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED    105   53
  DEL PEAK 12(5Q12.1) WILD-TYPE  343  109
        clus
vv       DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  COLON                          105                           343
  RECTUM                          53                           109
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 12(5Q12.1) MUTATED        25        0        8        35         1
  DEL PEAK 12(5Q12.1) WILD-TYPE      79        1       29       137        11
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 12(5Q12.1) MUTATED           0         4          8         19
  DEL PEAK 12(5Q12.1) WILD-TYPE         2        20          7         65
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 12(5Q12.1) MUTATED           20       20        12         1
  DEL PEAK 12(5Q12.1) WILD-TYPE         35       43        12         1
D36V4, multiclass
            clus
vv           DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  STAGE I                             25                            79
  STAGE IA                             0                             1
  STAGE II                             8                            29
  STAGE IIA                           35                           137
  STAGE IIB                            1                            11
  STAGE IIC                            0                             2
  STAGE III                            4                            20
  STAGE IIIA                           8                             7
  STAGE IIIB                          19                            65
  STAGE IIIC                          20                            35
  STAGE IV                            20                            43
  STAGE IVA                           12                            12
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 12(5Q12.1) MUTATED     5  29 107  17
  DEL PEAK 12(5Q12.1) WILD-TYPE  15  76 310  52
D36V5, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  T1                           5                            15
  T2                          29                            76
  T3                         107                           310
  T4                          17                            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 12(5Q12.1) MUTATED    76  44  38
  DEL PEAK 12(5Q12.1) WILD-TYPE 270 106  77
D36V6, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  N0                          76                           270
  N1                          44                           106
  N2                          38                            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"
D36V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED   104  32
  DEL PEAK 12(5Q12.1) WILD-TYPE 349  56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED    104   32
  DEL PEAK 12(5Q12.1) WILD-TYPE  349   56
   clus
vv  DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  0                         104                           349
  1                          32                            56
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED    71  87
  DEL PEAK 12(5Q12.1) WILD-TYPE 218 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED     71   87
  DEL PEAK 12(5Q12.1) WILD-TYPE  218  238
        clus
vv       DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  FEMALE                          71                           218
  MALE                            87                           238
[1] 2 2
[1] FALSE
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED   128   7
  DEL PEAK 12(5Q12.1) WILD-TYPE 354  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED    128    7
  DEL PEAK 12(5Q12.1) WILD-TYPE  354   22
     clus
vv    DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  NO                          128                           354
  YES                           7                            22
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                     97
  DEL PEAK 12(5Q12.1) WILD-TYPE                  285
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                               8
  DEL PEAK 12(5Q12.1) WILD-TYPE                            54
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                      50
  DEL PEAK 12(5Q12.1) WILD-TYPE                    96
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 12(5Q12.1) MUTATED                                2
  DEL PEAK 12(5Q12.1) WILD-TYPE                             11
D36V10, multiclass
                                clus
vv                               DEL PEAK 12(5Q12.1) MUTATED
  COLON ADENOCARCINOMA                                    97
  COLON MUCINOUS ADENOCARCINOMA                            8
  RECTAL ADENOCARCINOMA                                   50
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 12(5Q12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     285
  COLON MUCINOUS ADENOCARCINOMA                             54
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(5Q12.1) MUTATED   109   3   9   5
  DEL PEAK 12(5Q12.1) WILD-TYPE 337   3  28  24
D36V11, multiclass
    clus
vv   DEL PEAK 12(5Q12.1) MUTATED DEL PEAK 12(5Q12.1) WILD-TYPE
  R0                         109                           337
  R1                           3                             3
  R2                           9                            28
  RX                           5                            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"
D36V12, continuous
D36V13, binary
                               cls
clus                              0   1
  DEL PEAK 12(5Q12.1) MUTATED     3  97
  DEL PEAK 12(5Q12.1) WILD-TYPE   2 255
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(5Q12.1) MUTATED      3   97
  DEL PEAK 12(5Q12.1) WILD-TYPE    2  255
                        clus
vv                       DEL PEAK 12(5Q12.1) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          97
                        clus
vv                       DEL PEAK 12(5Q12.1) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           255
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 13(5Q21.2) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(5Q21.2) MUTATED   133  46
  DEL PEAK 13(5Q21.2) WILD-TYPE 333  82
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          179                           415 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                           46                            82 
$`DEL PEAK 13(5Q21.2) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3530 
       13.94        14.53        24.16         1.02        37.05        19.07 
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 
       13.02        19.99        19.00        85.05        31.07        24.03 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6625 
      106.75         1.94        49.08         5.88        63.62        91.79 
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-BM-6198 
       10.39        13.94        19.99        17.03        17.03        21.24 
TCGA-G5-6233 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2683 
       18.28         1.61        39.45        43.76        43.76        16.57 
TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 TCGA-A6-6140 
       37.02        36.53        30.44        29.19        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A56B 
       25.08        25.18        21.76        23.87        20.28        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3655 
        9.63         5.03        26.01        12.99        24.00        61.02 
TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3811 TCGA-AA-3841 
       50.04        47.01        15.02        11.01        10.06        36.95 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       37.02        10.06        33.07         0.99        31.07        17.03 
TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3994 TCGA-AA-A00F TCGA-AA-A00O 
       24.00         2.01        21.99        27.02        34.03        27.02 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02E 
       42.02        17.03        15.02        10.98        33.04         2.96 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
        2.01         5.03        41.00        22.42        27.42        26.47 
TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A71X TCGA-AZ-4614 
        0.46        16.31         0.20        21.44        19.33         5.65 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5797 
       65.00        62.79        29.56         5.23        12.69        12.59 
TCGA-CA-6719 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       14.30        25.02        26.04         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 
       22.03         5.03        15.02        14.04        29.03        13.02 
TCGA-CM-6677 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6922 
       11.08        19.59        20.42        15.12        17.85        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D9 
       12.43         9.04        13.41        11.38        92.75       140.38 
TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28H TCGA-DM-A28K 
       44.32         7.76        14.04        26.47       117.07        98.24 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6704 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 
        8.61        31.96         1.55        33.67         8.35        82.39 
TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 
       36.00        18.18        10.98        12.79        42.77         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 
       21.90        38.70        46.92        17.23        43.04        37.74 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3591 
       24.36        24.59        86.63        65.98        32.02        34.03 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 
       20.98         7.99        29.98        37.02        32.98        19.04 
TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 
       19.99         1.02        48.03        28.04        36.03         3.98 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-CI-6620 
        6.02        23.01         1.94        38.96        41.00        33.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       31.00        13.97        31.00        51.98        10.98        25.05 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6510 TCGA-EI-6513 
      126.44        57.24        51.48        20.55        18.28        16.34 
TCGA-EI-6881 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6864 
       16.41        13.64         9.96        28.57        12.46 

$`DEL PEAK 13(5Q21.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 
       24.33        45.60        58.03        13.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
        8.05        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        6.05         0.92        36.00        19.04        19.04        14.93 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 
       15.52        25.08        10.88        75.95       100.01        28.21 
TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       23.51        35.93        22.09        35.80        26.17        79.69 
TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       17.85         8.02        25.97        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       51.98        55.76        26.43        15.62         4.80        12.66 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
        9.53        46.65        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 
       35.11        37.05        37.25        34.65        32.75        32.45 
TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       32.91        31.63        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6652 
       32.71        29.16        22.52         8.38        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       24.39        20.12        19.66        16.24        24.92        61.84 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
        6.97         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
        0.00        29.00        29.00        14.01        33.99        21.01 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       29.95        20.98        13.94        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
        2.01        14.01        47.05         5.98        37.05         5.03 
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-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 
       15.95        38.99         0.00        17.03         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       36.03        32.05        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
        2.01        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A004 
       13.05        34.06        25.02        27.02         7.96        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01G 
        0.99        14.99        34.98        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02O 
        1.02        26.01        37.02        51.98        39.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       24.53         5.79        16.44         0.92        14.50        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK 
        0.95        33.01        17.82        17.26        17.85        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
      109.28        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6607 
       88.21        49.41         6.77        12.10        11.74         3.19 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5349 
       23.05        20.02        37.02        27.02        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       32.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 TCGA-CM-6171 
       16.04        21.99        14.99        12.99        15.02        14.04 
TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 
       11.01        12.95        13.05        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        45.40        54.61        56.09        55.92        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 
       17.75        18.25        25.48        43.27         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 
       12.49        16.14        15.58         7.53        12.39        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
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-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 TCGA-DM-A28C TCGA-DM-A28E 
        7.50       131.51       135.65       139.17        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       35.97        60.79        95.18        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 
        6.18        47.87        34.42        41.42        43.04        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 
        0.53        47.41        35.31       133.18        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       61.91        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW 
       19.33        19.33         9.93        15.65        16.80        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 
       32.98        31.30        60.13        11.90        70.03        39.48 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       13.55        37.97        34.49        29.98        16.83        20.02 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.84        36.03        12.00         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
       24.00         1.02        46.03        34.03        34.03         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-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99         0.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        25.02        32.02        19.99 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 
       14.04         1.02        46.03        20.98        13.94        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 
        9.07         1.02         1.02        49.97        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        6.05        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 
        7.17        21.01        25.05        26.04        12.00        44.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF 
       25.97        25.05        12.62        41.36       129.27        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         3.48         4.18        19.96        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.31         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46        11.97         8.45        49.51        42.35         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-G5-6572 
       47.08 

  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                       140.38                        148.01 
  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE 
                        21.90                         22.06 
[1] "0.2 - 140.4 (21.9)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D37V2, continuous
D37V3, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED   131  55
  DEL PEAK 13(5Q21.2) WILD-TYPE 317 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED    131   55
  DEL PEAK 13(5Q21.2) WILD-TYPE  317  107
        clus
vv       DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  COLON                          131                           317
  RECTUM                          55                           107
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 13(5Q21.2) MUTATED        26        0        9        41         1
  DEL PEAK 13(5Q21.2) WILD-TYPE      78        1       28       131        11
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 13(5Q21.2) MUTATED           0         5          9         29
  DEL PEAK 13(5Q21.2) WILD-TYPE         2        19          6         55
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 13(5Q21.2) MUTATED           23       24        13         1
  DEL PEAK 13(5Q21.2) WILD-TYPE         32       39        11         1
D37V4, multiclass
            clus
vv           DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  STAGE I                             26                            78
  STAGE IA                             0                             1
  STAGE II                             9                            28
  STAGE IIA                           41                           131
  STAGE IIB                            1                            11
  STAGE IIC                            0                             2
  STAGE III                            5                            19
  STAGE IIIA                           9                             6
  STAGE IIIB                          29                            55
  STAGE IIIC                          23                            32
  STAGE IV                            24                            39
  STAGE IVA                           13                            11
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 13(5Q21.2) MUTATED     4  32 129  21
  DEL PEAK 13(5Q21.2) WILD-TYPE  16  73 288  48
D37V5, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  T1                           4                            16
  T2                          32                            73
  T3                         129                           288
  T4                          21                            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 13(5Q21.2) MUTATED    85  56  45
  DEL PEAK 13(5Q21.2) WILD-TYPE 261  94  70
D37V6, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  N0                          85                           261
  N1                          56                            94
  N2                          45                            70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED   126  37
  DEL PEAK 13(5Q21.2) WILD-TYPE 327  51
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED    126   37
  DEL PEAK 13(5Q21.2) WILD-TYPE  327   51
   clus
vv  DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  0                         126                           327
  1                          37                            51
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED    86 100
  DEL PEAK 13(5Q21.2) WILD-TYPE 203 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED     86  100
  DEL PEAK 13(5Q21.2) WILD-TYPE  203  225
        clus
vv       DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  FEMALE                          86                           203
  MALE                           100                           225
[1] 2 2
[1] FALSE
D37V9, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED   146   8
  DEL PEAK 13(5Q21.2) WILD-TYPE 336  21
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED    146    8
  DEL PEAK 13(5Q21.2) WILD-TYPE  336   21
     clus
vv    DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  NO                          146                           336
  YES                           8                            21
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 13(5Q21.2) MUTATED                    117
  DEL PEAK 13(5Q21.2) WILD-TYPE                  265
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 13(5Q21.2) MUTATED                              14
  DEL PEAK 13(5Q21.2) WILD-TYPE                            48
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 13(5Q21.2) MUTATED                      53
  DEL PEAK 13(5Q21.2) WILD-TYPE                    93
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 13(5Q21.2) MUTATED                                1
  DEL PEAK 13(5Q21.2) WILD-TYPE                             12
D37V10, multiclass
                                clus
vv                               DEL PEAK 13(5Q21.2) MUTATED
  COLON ADENOCARCINOMA                                   117
  COLON MUCINOUS ADENOCARCINOMA                           14
  RECTAL ADENOCARCINOMA                                   53
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 13(5Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     265
  COLON MUCINOUS ADENOCARCINOMA                             48
  RECTAL ADENOCARCINOMA                                     93
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 13(5Q21.2) MUTATED   126   3  13   7
  DEL PEAK 13(5Q21.2) WILD-TYPE 320   3  24  22
D37V11, multiclass
    clus
vv   DEL PEAK 13(5Q21.2) MUTATED DEL PEAK 13(5Q21.2) WILD-TYPE
  R0                         126                           320
  R1                           3                             3
  R2                          13                            24
  RX                           7                            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
D37V13, binary
                               cls
clus                              0   1
  DEL PEAK 13(5Q21.2) MUTATED     3 109
  DEL PEAK 13(5Q21.2) WILD-TYPE   2 243
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(5Q21.2) MUTATED      3  109
  DEL PEAK 13(5Q21.2) WILD-TYPE    2  243
                        clus
vv                       DEL PEAK 13(5Q21.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         109
                        clus
vv                       DEL PEAK 13(5Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           243
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 14(5Q22.2) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(5Q22.2) MUTATED   131  47
  DEL PEAK 14(5Q22.2) WILD-TYPE 335  81
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          178                           416 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                           47                            81 
$`DEL PEAK 14(5Q22.2) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3522 TCGA-AA-3530 
       13.94        14.53        24.16         1.02        37.05        19.07 
TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3867 
       13.02        19.99        19.00        85.05        19.04        24.03 
TCGA-AA-3986 TCGA-AD-6964 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       19.07        10.88       106.75         1.94        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6625 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       63.62        91.79        10.39        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-BM-6198 TCGA-G5-6233 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       17.03        21.24        18.28         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2683 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 
       43.76        16.57        37.02        36.53        30.44        29.19 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 
       27.09        24.13        25.08        25.18        21.76        23.87 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 
        9.63         5.03         1.02        26.01        12.99        24.00 
TCGA-AA-3655 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3811 TCGA-AA-3841 
       61.02        50.04        47.01        15.02        10.06        36.95 
TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       37.02        10.06        33.07         0.99        31.07        17.03 
TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q 
       24.00         2.01        21.99        34.03        27.02        42.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J 
       15.02        10.98        33.04         2.96         2.01         5.03 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 
       41.00        22.42        27.42        26.47        16.31         0.20 
TCGA-AY-6197 TCGA-AY-A71X TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6599 
       21.44        19.33         5.65        65.00        62.79         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6719 TCGA-CK-6751 
       29.56         5.23        12.46        12.59        14.30       124.27 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 
       25.02        26.04         8.02        13.02        22.03         5.03 
TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6677 TCGA-D5-5539 
       15.02        14.04        29.03        13.02        11.08        19.59 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 
       15.12        17.85        10.13        12.43         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1D4 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 TCGA-DM-A28A 
       11.38        92.75       140.38        44.32         7.76        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        31.96         1.55 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A50T TCGA-NH-A50U 
       33.67         8.35        82.39        36.00        18.18        10.98 
TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2687 
       12.79        42.77         8.42        21.90        38.70        46.92 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56K 
       17.23        43.04        37.74        24.36        24.59        86.63 
TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 
       65.98        32.02        34.03        20.98        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 
       32.98        19.04        19.99         1.02        48.03        28.04 
TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G 
       36.03         3.98         6.02        23.01         1.94        38.96 
TCGA-AG-A02X TCGA-AH-6903 TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
       41.00        19.46        33.17         7.17        31.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC 
       31.00        51.98        10.98        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6513 
       57.24        51.48        20.55        19.96        18.28        16.34 
TCGA-EI-6881 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6864 
       16.41         9.96        28.57        12.46 

$`DEL PEAK 14(5Q22.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 
       24.33        45.60        58.03        13.02        24.03        36.03 
TCGA-AA-3525 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
        8.05        34.03         0.99        17.95        23.01        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        6.05         0.92        36.00        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       24.00        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 
       25.08        75.95       100.01        28.21        23.51        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 
       22.09        35.80        26.17        79.69        17.85         8.02 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
       25.97        15.95        36.03        31.00        51.98        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 
       26.43        15.62         4.80        12.66         9.53        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 
       43.43        42.90        42.28        44.91        35.11        37.05 
TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        34.65        32.75        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-A6-6141 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       22.52         8.38        20.61        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B 
       19.66        20.28        16.24        24.92        61.84        56.25 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        7.04         3.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 
       29.00        29.00        14.01        33.99        21.01        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       20.98        13.94        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       14.01        47.05        11.01         5.98        37.05         5.03 
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-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3852 
       15.95        38.99         0.00        17.03         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
       36.03        32.05        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
        2.01        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         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-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
        4.01         0.99        17.03        14.99        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-A029 
       35.01         1.02         1.02        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
       39.98         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 
       12.16        83.24        24.53         5.79        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6386 
        0.92        14.50        27.09         0.95        33.01        17.82 
TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        17.85        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6600 
       32.94         5.13        22.36        88.21        49.41        12.10 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 
       11.74         3.19        12.69        12.36        12.39        12.59 
TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.20        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
TCGA-CK-6748 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4751 TCGA-CM-5341 
        2.01        23.05        20.02        37.02        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        32.02        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-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       15.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       11.01        10.06        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        7.53        12.39        14.30         9.44        11.64        13.35 
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-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91        13.32        12.59         7.50       131.51       135.65 
TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28M 
      139.17        14.04        81.37       119.93        35.97        95.18 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 
       11.11        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
      133.18        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 
       55.04        85.48        39.42        61.91        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       13.78        46.75        74.79        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO 
       15.65        16.80        29.46        32.98        31.30        60.13 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       11.90        70.03        39.48        13.55        37.97        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       29.98        16.83        20.02        11.84        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        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-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 
       14.01        25.02        32.02        19.99        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98        13.94        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.02        49.97        61.97        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 
       43.20        27.55        26.43         6.05        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       47.44        48.20        78.12        21.01        25.05        26.04 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DE 
       12.00        44.02        25.97        25.05        12.62       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 
       24.13        32.61         3.48         4.18        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         8.45        49.51        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-G5-6572 
       11.87        47.08 

  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                       140.38                        148.01 
  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE 
                       21.830                        22.075 
[1] "0.2 - 140.4 (21.8)" "0.0 - 148.0 (22.1)"
[1] "hr=" "1.3"
D38V2, continuous
D38V3, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   129  59
  DEL PEAK 14(5Q22.2) WILD-TYPE 319 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    129   59
  DEL PEAK 14(5Q22.2) WILD-TYPE  319  103
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  COLON                          129                           319
  RECTUM                          59                           103
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 14(5Q22.2) MUTATED        27        0       10        45         0
  DEL PEAK 14(5Q22.2) WILD-TYPE      77        1       27       127        12
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 14(5Q22.2) MUTATED           0         5          8         28
  DEL PEAK 14(5Q22.2) WILD-TYPE         2        19          7         56
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 14(5Q22.2) MUTATED           22       24        12         1
  DEL PEAK 14(5Q22.2) WILD-TYPE         33       39        12         1
D38V4, multiclass
            clus
vv           DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  STAGE I                             27                            77
  STAGE IA                             0                             1
  STAGE II                            10                            27
  STAGE IIA                           45                           127
  STAGE IIB                            0                            12
  STAGE IIC                            0                             2
  STAGE III                            5                            19
  STAGE IIIA                           8                             7
  STAGE IIIB                          28                            56
  STAGE IIIC                          22                            33
  STAGE IV                            24                            39
  STAGE IVA                           12                            12
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 14(5Q22.2) MUTATED     4  32 132  20
  DEL PEAK 14(5Q22.2) WILD-TYPE  16  73 285  49
D38V5, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  T1                           4                            16
  T2                          32                            73
  T3                         132                           285
  T4                          20                            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 14(5Q22.2) MUTATED    92  53  43
  DEL PEAK 14(5Q22.2) WILD-TYPE 254  97  72
D38V6, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  N0                          92                           254
  N1                          53                            97
  N2                          43                            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"
D38V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   126  36
  DEL PEAK 14(5Q22.2) WILD-TYPE 327  52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    126   36
  DEL PEAK 14(5Q22.2) WILD-TYPE  327   52
   clus
vv  DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  0                         126                           327
  1                          36                            52
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED    83 105
  DEL PEAK 14(5Q22.2) WILD-TYPE 206 220
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED     83  105
  DEL PEAK 14(5Q22.2) WILD-TYPE  206  220
        clus
vv       DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  FEMALE                          83                           206
  MALE                           105                           220
[1] 2 2
[1] FALSE
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED   143   9
  DEL PEAK 14(5Q22.2) WILD-TYPE 339  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED    143    9
  DEL PEAK 14(5Q22.2) WILD-TYPE  339   20
     clus
vv    DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  NO                          143                           339
  YES                           9                            20
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                    116
  DEL PEAK 14(5Q22.2) WILD-TYPE                  266
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                              13
  DEL PEAK 14(5Q22.2) WILD-TYPE                            49
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                      56
  DEL PEAK 14(5Q22.2) WILD-TYPE                    90
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 14(5Q22.2) MUTATED                                2
  DEL PEAK 14(5Q22.2) WILD-TYPE                             11
D38V10, multiclass
                                clus
vv                               DEL PEAK 14(5Q22.2) MUTATED
  COLON ADENOCARCINOMA                                   116
  COLON MUCINOUS ADENOCARCINOMA                           13
  RECTAL ADENOCARCINOMA                                   56
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 14(5Q22.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     266
  COLON MUCINOUS ADENOCARCINOMA                             49
  RECTAL ADENOCARCINOMA                                     90
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(5Q22.2) MUTATED   123   3  15   8
  DEL PEAK 14(5Q22.2) WILD-TYPE 323   3  22  21
D38V11, multiclass
    clus
vv   DEL PEAK 14(5Q22.2) MUTATED DEL PEAK 14(5Q22.2) WILD-TYPE
  R0                         123                           323
  R1                           3                             3
  R2                          15                            22
  RX                           8                            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"
D38V12, continuous
D38V13, binary
                               cls
clus                              0   1
  DEL PEAK 14(5Q22.2) MUTATED     3 109
  DEL PEAK 14(5Q22.2) WILD-TYPE   2 243
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(5Q22.2) MUTATED      3  109
  DEL PEAK 14(5Q22.2) WILD-TYPE    2  243
                        clus
vv                       DEL PEAK 14(5Q22.2) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                         109
                        clus
vv                       DEL PEAK 14(5Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           243
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 15(5Q23.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(5Q23.3) MUTATED   115  38
  DEL PEAK 15(5Q23.3) WILD-TYPE 351  90
  DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE 
                          153                           441 
  DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE 
                           38                            90 
$`DEL PEAK 15(5Q23.3) MUTATED`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3560 
       13.94        14.53        24.16        37.05        13.02        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3867 TCGA-AD-6964 TCGA-AZ-4681 
       19.99        19.00        85.05        24.03        10.88       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-3890 
        1.94        49.08         5.88        91.79        13.94        17.03 
TCGA-AG-4008 TCGA-BM-6198 TCGA-G5-6233 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       17.03        21.24        18.28         1.61        39.45        43.76 
TCGA-A6-2674 TCGA-A6-2686 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-6137 
       43.76        37.02        36.53        30.44        29.19        27.09 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A5ZU TCGA-AA-3488 
       25.08        25.18        21.76        23.87         9.63         5.03 
TCGA-AA-3494 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3673 TCGA-AA-3678 
        1.02        26.01        12.99        24.00        50.04        47.01 
TCGA-AA-3811 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 
       10.06        36.95        37.02        33.07         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00O 
       17.03        24.00         2.01        21.99        34.03        27.02 
TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02H 
       42.02        15.02        10.98        33.04         2.96         2.01 
TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 
       41.00        22.42        27.42        26.47        16.31         0.20 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5797 
        5.65        65.00        62.79        29.56         5.23        12.59 
TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5864 
       14.30         8.02        13.02        22.03         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6677 TCGA-D5-5539 
       14.04        29.03        13.02        15.02        11.08        19.59 
TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 
       15.12        17.85        10.13        12.43         9.04        13.41 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A28A TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      140.38        44.32        26.47       117.07        98.24         8.61 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 
        1.55        43.04        33.67         8.35        82.39        36.00 
TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       18.18        10.98        42.77        32.98         8.42        21.90 
TCGA-RU-A8FL TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 
       38.70        46.92        17.23        43.04        37.74        24.36 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3725 
       24.59        86.63        65.98        32.02        34.03        20.98 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 
       29.98        37.02        32.98        19.04        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A026 
       48.03        28.04        36.03         3.98        23.01         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6903 TCGA-CI-6620 TCGA-DC-4745 TCGA-DC-5869 
       38.96        41.00        19.46        33.17        21.01        31.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA 
       13.97        31.00        51.98        10.98        25.05       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6513 
       41.36        57.24        51.48        20.55        20.91        16.34 
TCGA-EI-6881 TCGA-F5-6464 TCGA-F5-6702 
       16.41         9.96        28.57 

$`DEL PEAK 15(5Q23.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60         1.02        58.03        13.02        24.03 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 
       36.03         8.05        19.07        34.03         0.99        17.95 
TCGA-AA-3556 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       23.01         6.05         0.92        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       14.93        31.07        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       50.99        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AZ-4313 TCGA-AZ-6601 
       39.06        21.37        15.52        25.08        75.95       100.01 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 
       26.17        79.69        17.85        10.39         8.02        19.99 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
       25.97        15.95        36.03        31.00        51.98        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 
       26.43        15.62         4.80        12.66         9.53        46.65 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        34.65        32.75        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6650 TCGA-A6-6652 
       29.16        22.52        24.13         8.38        20.61        24.69 
TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       24.39        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
       61.84        56.25         7.04         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 
       19.07         0.00        29.00        29.00        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3679 
        6.97        54.02         2.01        14.01        47.05        15.02 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       11.01         5.98        37.05         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 
        0.99        25.02         1.02        17.98        15.95        38.99 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06         0.00         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       32.05        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 
       33.01        26.01        20.98        34.03        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01F 
        0.99        17.03        14.99        34.98        15.02        32.02 
TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       12.00        31.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
        1.02         1.02        26.01        37.02        51.98        39.98 
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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-A5EK TCGA-AM-5820 
       12.16        83.24        24.53         5.79        16.44         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        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41        32.94         5.13        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       49.41         6.77        12.10        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.36        12.46        12.39        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         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        25.02        26.04        27.02 
TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       29.06        22.98        30.08        32.02        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-6676 
       12.99        14.04        11.01        12.95        13.05        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        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       55.92        20.19        20.42        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       43.27         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        7.53        12.39        14.30         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.00        11.38        10.26       119.70        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1DA 
      130.65        92.75        49.91        13.32        12.59         7.50 
TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C 
      131.51       135.65         7.76       139.17        14.04        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
      119.93        35.97        60.79        95.18        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 
       35.74        35.74         6.18        47.87        34.42        41.42 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       13.25         0.53        47.41        35.31       133.18        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       39.42        61.91        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       74.79        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 
       16.80        29.46        31.30        60.13        11.90        70.03 
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       39.48        13.55        37.97        34.49        29.98        16.83 
TCGA-AF-6655 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       20.02        11.84        36.03        12.00         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        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-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
       19.99         7.99         0.99         0.99         0.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 
       17.95        36.95        13.02        35.01        14.01        25.02 
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        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       49.97        61.97        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       27.55        26.43         6.05        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       48.20        78.12         7.17        25.05        26.04        12.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF 
       44.02        25.97        25.05        12.62       129.27        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 
       32.61         3.48         4.18        19.96        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         8.45        49.51        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE 
                       140.38                        148.01 
  DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE 
                        23.87                         21.44 
[1] "0.2 - 140.4 (23.9)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.2"
D39V2, continuous
D39V3, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.3) MUTATED   107  53
  DEL PEAK 15(5Q23.3) WILD-TYPE 341 109
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.3) MUTATED    107   53
  DEL PEAK 15(5Q23.3) WILD-TYPE  341  109
        clus
vv       DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE
  COLON                          107                           341
  RECTUM                          53                           109
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 15(5Q23.3) MUTATED        23        0        8        37         0
  DEL PEAK 15(5Q23.3) WILD-TYPE      81        1       29       135        12
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 15(5Q23.3) MUTATED           0         4          8         23
  DEL PEAK 15(5Q23.3) WILD-TYPE         2        20          7         61
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 15(5Q23.3) MUTATED           23       18        11         0
  DEL PEAK 15(5Q23.3) WILD-TYPE         32       45        13         2
D39V4, multiclass
            clus
vv           DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE
  STAGE I                             23                            81
  STAGE IA                             0                             1
  STAGE II                             8                            29
  STAGE IIA                           37                           135
  STAGE IIB                            0                            12
  STAGE IIC                            0                             2
  STAGE III                            4                            20
  STAGE IIIA                           8                             7
  STAGE IIIB                          23                            61
  STAGE IIIC                          23                            32
  STAGE IV                            18                            45
  STAGE IVA                           11                            13
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 15(5Q23.3) MUTATED     4  27 113  16
  DEL PEAK 15(5Q23.3) WILD-TYPE  16  78 304  53
D39V5, multiclass
    clus
vv   DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE
  T1                           4                            16
  T2                          27                            78
  T3                         113                           304
  T4                          16                            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 15(5Q23.3) MUTATED    74  46  40
  DEL PEAK 15(5Q23.3) WILD-TYPE 272 104  75
D39V6, multiclass
    clus
vv   DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE
  N0                          74                           272
  N1                          46                           104
  N2                          40                            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"
D39V7, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.3) MUTATED   110  28
  DEL PEAK 15(5Q23.3) WILD-TYPE 343  60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.3) MUTATED    110   28
  DEL PEAK 15(5Q23.3) WILD-TYPE  343   60
   clus
vv  DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE
  0                         110                           343
  1                          28                            60
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.3) MUTATED    73  87
  DEL PEAK 15(5Q23.3) WILD-TYPE 216 238
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.3) MUTATED     73   87
  DEL PEAK 15(5Q23.3) WILD-TYPE  216  238
        clus
vv       DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE
  FEMALE                          73                           216
  MALE                            87                           238
[1] 2 2
[1] FALSE
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.3) MUTATED   126   6
  DEL PEAK 15(5Q23.3) WILD-TYPE 356  23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.3) MUTATED    126    6
  DEL PEAK 15(5Q23.3) WILD-TYPE  356   23
     clus
vv    DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE
  NO                          126                           356
  YES                           6                            23
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 15(5Q23.3) MUTATED                     98
  DEL PEAK 15(5Q23.3) WILD-TYPE                  284
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(5Q23.3) MUTATED                               9
  DEL PEAK 15(5Q23.3) WILD-TYPE                            53
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 15(5Q23.3) MUTATED                      50
  DEL PEAK 15(5Q23.3) WILD-TYPE                    96
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 15(5Q23.3) MUTATED                                2
  DEL PEAK 15(5Q23.3) WILD-TYPE                             11
D39V10, multiclass
                                clus
vv                               DEL PEAK 15(5Q23.3) MUTATED
  COLON ADENOCARCINOMA                                    98
  COLON MUCINOUS ADENOCARCINOMA                            9
  RECTAL ADENOCARCINOMA                                   50
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 15(5Q23.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     284
  COLON MUCINOUS ADENOCARCINOMA                             53
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 15(5Q23.3) MUTATED   106   3  11   6
  DEL PEAK 15(5Q23.3) WILD-TYPE 340   3  26  23
D39V11, multiclass
    clus
vv   DEL PEAK 15(5Q23.3) MUTATED DEL PEAK 15(5Q23.3) WILD-TYPE
  R0                         106                           340
  R1                           3                             3
  R2                          11                            26
  RX                           6                            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"
D39V12, continuous
D39V13, binary
                               cls
clus                              0   1
  DEL PEAK 15(5Q23.3) MUTATED     3  94
  DEL PEAK 15(5Q23.3) WILD-TYPE   2 258
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(5Q23.3) MUTATED      3   94
  DEL PEAK 15(5Q23.3) WILD-TYPE    2  258
                        clus
vv                       DEL PEAK 15(5Q23.3) MUTATED
  HISPANIC OR LATINO                               3
  NOT HISPANIC OR LATINO                          94
                        clus
vv                       DEL PEAK 15(5Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           258
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 16(6P25.3) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(6P25.3) MUTATED    59  18
  DEL PEAK 16(6P25.3) WILD-TYPE 407 110
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           77                           517 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                           18                           110 
$`DEL PEAK 16(6P25.3) MUTATED`
TCGA-A6-6649 TCGA-AA-3692 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3939 TCGA-AD-6895 
       24.16        36.00        19.04        29.98        12.99        25.08 
TCGA-AD-6964 TCGA-AG-3611 TCGA-BM-6198 TCGA-A6-2671 TCGA-A6-2683 TCGA-A6-2686 
       10.88        13.94        21.24        43.76        16.57        37.02 
TCGA-A6-6648 TCGA-A6-6782 TCGA-AA-3518 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       25.18        20.28         1.02        13.94        61.02         6.97 
TCGA-AA-3666 TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3858 TCGA-AA-3864 
        2.01        37.05        38.99        36.95        31.07        53.00 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3966 TCGA-AA-A004 TCGA-AA-A00E TCGA-AA-A00J 
       18.05        24.00         2.01        13.94        30.02        18.05 
TCGA-AA-A00O TCGA-AA-A01P TCGA-AA-A01X TCGA-AA-A02O TCGA-AD-6899 TCGA-AD-A5EK 
       27.02        38.07        26.01         0.92         5.79        16.44 
TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-5341 
        5.65         3.19        12.69        12.36        12.46        29.06 
TCGA-CM-5348 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 
       22.98        11.08        11.01        45.40        20.19        17.75 
TCGA-D5-6536 TCGA-D5-6898 TCGA-DM-A1D7 TCGA-DM-A28A TCGA-DM-A28H TCGA-F4-6808 
       17.85         7.53        13.32        26.47       117.07        33.67 
TCGA-G4-6317 TCGA-T9-A92H TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       36.00        11.90        17.23        13.55        37.97        34.49 
TCGA-AF-4110 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 
       29.98        24.00        34.03        34.03        34.03        50.04 
TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A011 TCGA-CI-6621 TCGA-DC-4745 
       36.03         3.98        13.94        37.02        13.78        21.01 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6511 TCGA-EI-6883 
       25.05        12.62        24.13        15.85        11.51 

$`DEL PEAK 16(6P25.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 
       34.03         0.99        13.02        17.95        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 
       19.99         6.05         0.92        19.00        85.05        19.04 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       14.93        31.07        24.03        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       21.37        15.52        75.95       106.75       100.01         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
       49.08         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 
       26.43        15.62         4.80        12.66         1.61         9.53 
TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 
       39.45        46.65        43.76        43.43        42.90        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-3809 
       44.91        35.11        37.05        37.25        34.65        32.75 
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-A6-5664 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-A6-6650 
       27.09        22.52        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-A565 TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       16.24        24.92        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        6.97         1.02        38.99         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       29.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3660 TCGA-AA-3664 
       21.01        24.00        29.95        20.98        78.08        54.02 
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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 
       25.02         1.02        17.98        15.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 
       32.05         0.99        17.03        27.02        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00Q 
       38.04        19.00        34.03        18.05         4.01        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-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01Q 
       10.98        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-A029 
       35.01         1.02        33.04         1.02        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02W 
        2.96        39.98         2.01         5.03        22.03        41.00 
TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 
       22.42        27.42        26.47         0.46         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       58.39         1.41        32.94         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       62.79        88.21        49.41         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        5.23        11.74        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
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        25.02 
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 
       32.02        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        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        15.12         4.80        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        13.35        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-A288 TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        14.04        81.37       119.93 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
       35.97        60.79        98.24        95.18         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       11.11        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       61.91        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       18.18        10.98        19.33        19.33         9.93        15.65 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 
       12.79        16.80        42.77        29.46        32.98         8.42 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2687 
       31.30        21.90        38.70        60.13        70.03        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       39.48        43.04        37.74        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       32.02         7.07        36.03        20.05         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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98         6.02        23.01         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       19.46         6.05        33.17        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       25.05       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-6508 
       32.61         3.48         4.18        20.55        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-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-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                         0.92                          0.00 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                       117.07                        148.01 
  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE 
                        21.01                         22.03 
[1] "0.9 - 117.1 (21.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D40V2, continuous
D40V3, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    55  21
  DEL PEAK 16(6P25.3) WILD-TYPE 393 141
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     55   21
  DEL PEAK 16(6P25.3) WILD-TYPE  393  141
        clus
vv       DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  COLON                           55                           393
  RECTUM                          21                           141
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 16(6P25.3) MUTATED         9        0        7        29         1
  DEL PEAK 16(6P25.3) WILD-TYPE      95        1       30       143        11
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 16(6P25.3) MUTATED           1         3          1          8
  DEL PEAK 16(6P25.3) WILD-TYPE         1        21         14         76
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 16(6P25.3) MUTATED            7        7         5         0
  DEL PEAK 16(6P25.3) WILD-TYPE         48       56        19         2
D40V4, multiclass
            clus
vv           DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  STAGE I                              9                            95
  STAGE IA                             0                             1
  STAGE II                             7                            30
  STAGE IIA                           29                           143
  STAGE IIB                            1                            11
  STAGE IIC                            1                             1
  STAGE III                            3                            21
  STAGE IIIA                           1                            14
  STAGE IIIB                           8                            76
  STAGE IIIC                           7                            48
  STAGE IV                             7                            56
  STAGE IVA                            5                            19
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 16(6P25.3) MUTATED     2   9  58  10
  DEL PEAK 16(6P25.3) WILD-TYPE  18  96 359  59
D40V5, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  T1                           2                            18
  T2                           9                            96
  T3                          58                           359
  T4                          10                            59
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 16(6P25.3) MUTATED    48  15  16
  DEL PEAK 16(6P25.3) WILD-TYPE 298 135  99
D40V6, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  N0                          48                           298
  N1                          15                           135
  N2                          16                            99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    57  11
  DEL PEAK 16(6P25.3) WILD-TYPE 396  77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     57   11
  DEL PEAK 16(6P25.3) WILD-TYPE  396   77
   clus
vv  DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  0                          57                           396
  1                          11                            77
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    29  50
  DEL PEAK 16(6P25.3) WILD-TYPE 260 275
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     29   50
  DEL PEAK 16(6P25.3) WILD-TYPE  260  275
        clus
vv       DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  FEMALE                          29                           260
  MALE                            50                           275
[1] 2 2
[1] FALSE
D40V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED    60   7
  DEL PEAK 16(6P25.3) WILD-TYPE 422  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED     60    7
  DEL PEAK 16(6P25.3) WILD-TYPE  422   22
     clus
vv    DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  NO                           60                           422
  YES                           7                            22
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 16(6P25.3) MUTATED                     49
  DEL PEAK 16(6P25.3) WILD-TYPE                  333
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(6P25.3) MUTATED                               5
  DEL PEAK 16(6P25.3) WILD-TYPE                            57
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 16(6P25.3) MUTATED                      18
  DEL PEAK 16(6P25.3) WILD-TYPE                   128
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 16(6P25.3) MUTATED                                3
  DEL PEAK 16(6P25.3) WILD-TYPE                             10
D40V10, multiclass
                                clus
vv                               DEL PEAK 16(6P25.3) MUTATED
  COLON ADENOCARCINOMA                                    49
  COLON MUCINOUS ADENOCARCINOMA                            5
  RECTAL ADENOCARCINOMA                                   18
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK 16(6P25.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     333
  COLON MUCINOUS ADENOCARCINOMA                             57
  RECTAL ADENOCARCINOMA                                    128
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(6P25.3) MUTATED    57   0   3   6
  DEL PEAK 16(6P25.3) WILD-TYPE 389   6  34  23
D40V11, multiclass
    clus
vv   DEL PEAK 16(6P25.3) MUTATED DEL PEAK 16(6P25.3) WILD-TYPE
  R0                          57                           389
  R1                           0                             6
  R2                           3                            34
  RX                           6                            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"
D40V12, continuous
D40V13, binary
                               cls
clus                              0   1
  DEL PEAK 16(6P25.3) MUTATED     0  42
  DEL PEAK 16(6P25.3) WILD-TYPE   5 310
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(6P25.3) MUTATED      0   42
  DEL PEAK 16(6P25.3) WILD-TYPE    5  310
                        clus
vv                       DEL PEAK 16(6P25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          42
                        clus
vv                       DEL PEAK 16(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           310
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 17(6Q26) MUTATION ANALYSIS
D41V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 17(6Q26) MUTATED    63  24
  DEL PEAK 17(6Q26) WILD-TYPE 403 104
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         87                         507 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                         24                         104 
$`DEL PEAK 17(6Q26) MUTATED`
TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3715 
       45.60        24.16        13.02        36.00        85.05        19.04 
TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3952 TCGA-AG-3611 TCGA-G5-6233 TCGA-G5-6641 
       31.07        12.99         2.01        13.94        18.28        26.43 
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-4107 TCGA-A6-6138 TCGA-A6-6782 TCGA-AA-3488 
       43.76        42.28        32.45        22.52        20.28         5.03 
TCGA-AA-3655 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3837 
       61.02        54.02         2.01        11.01        37.05        38.99 
TCGA-AA-3841 TCGA-AA-3854 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-A00J TCGA-AA-A00U 
       36.95        36.03        18.05        24.00        18.05        17.03 
TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AD-6899 
       10.98        33.04        26.01         2.96         2.01         5.79 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4616 
       16.44         0.46        16.31         0.20        18.84         5.13 
TCGA-AZ-6598 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CM-6172 
       49.41         3.19        12.69        12.36        12.46        11.01 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6531 
       13.05        11.08        11.01        45.40        20.19        17.75 
TCGA-D5-6535 TCGA-D5-6898 TCGA-DM-A1D7 TCGA-DM-A1HA TCGA-F4-6704 TCGA-F4-6808 
       15.12         7.53        13.32       131.51         1.55        33.67 
TCGA-G4-6297 TCGA-NH-A6GA TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       82.39         9.93        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3587 
       34.49        37.74        12.00        32.02        24.00        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-4005 
       34.03        34.03         2.01         6.05        19.99        14.04 
TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A011 TCGA-AH-6544 TCGA-AH-6644 TCGA-CI-6623 
        1.02        13.94        37.02        38.56        27.55        47.44 
TCGA-DC-6682 TCGA-DT-5265 TCGA-F5-6863 
       25.05        12.62        11.87 

$`DEL PEAK 17(6Q26) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        14.53         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
        0.99        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3844 TCGA-AA-3867 TCGA-AA-3870 
        0.92        19.00        19.04        14.93        24.03        29.98 
TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       24.00        50.99        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
       19.99        17.03        17.03        25.97        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T 
       31.00        51.98        21.24        55.76        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 
       12.66         1.61         9.53        39.45        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.43        42.90        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       37.25        37.02        34.65        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       31.63        30.44        29.19        33.53        23.61        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       56.25         9.63         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 
       35.01        63.98         6.97         1.02        38.99         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
        9.07        19.07         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       12.99        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3667 TCGA-AA-3673 
       20.98        13.94        78.08         6.97        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.05        47.01        15.02         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       15.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        32.05         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       17.03        27.02        31.00         2.01        33.01        26.01 
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-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        34.03        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02        42.02         0.99        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02         1.02        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6901 
       18.05        40.96        12.16        83.24        24.53        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 
       27.42        26.47         0.92        14.50        27.09         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X 
       33.01        21.44        17.82        17.26        17.85        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 
      109.28        58.39         1.41         5.65        32.94        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 
       65.00        62.79        88.21         6.77        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        5.23        11.74        12.39        12.59        12.59        12.20 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
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        25.02 
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        32.02        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-6674 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       14.04        12.95        11.08        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        20.42        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        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        13.35        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-A1HB 
       49.91        12.59       140.38         7.50        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 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
       35.31       133.18         8.35        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       18.18        10.98        19.33        19.33        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       21.90        38.70        60.13        11.90        70.03        46.92 
TCGA-AF-2689 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       39.48        29.98        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 
       86.63        65.98        11.84        36.03         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       20.05         1.02        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 
        3.98        46.03        20.98         6.02        23.01         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        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         2.50        43.20        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       25.05       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-6507 
       51.48        32.61         3.48         4.18        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-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       38.14        12.46        47.08 

  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                        0.2                         0.0 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                     131.51                      148.01 
  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE 
                      18.28                       22.36 
[1] "0.2 - 131.5 (18.3)" "0.0 - 148.0 (22.4)"
[1] "hr=" "1.6"
D41V2, continuous
D41V3, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    61  28
  DEL PEAK 17(6Q26) WILD-TYPE 387 134
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     61   28
  DEL PEAK 17(6Q26) WILD-TYPE  387  134
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  COLON                         61                         387
  RECTUM                        28                         134
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 17(6Q26) MUTATED        13        0        9        20         1
  DEL PEAK 17(6Q26) WILD-TYPE      91        1       28       152        11
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 17(6Q26) MUTATED           0         3          1         10
  DEL PEAK 17(6Q26) WILD-TYPE         2        21         14         74
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 17(6Q26) MUTATED           14       12         4         1
  DEL PEAK 17(6Q26) WILD-TYPE         41       51        20         1
D41V4, multiclass
            clus
vv           DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  STAGE I                           13                          91
  STAGE IA                           0                           1
  STAGE II                           9                          28
  STAGE IIA                         20                         152
  STAGE IIB                          1                          11
  STAGE IIC                          0                           2
  STAGE III                          3                          21
  STAGE IIIA                         1                          14
  STAGE IIIB                        10                          74
  STAGE IIIC                        14                          41
  STAGE IV                          12                          51
  STAGE IVA                          4                          20
  STAGE IVB                          1                           1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 17(6Q26) MUTATED     5  10  64  12
  DEL PEAK 17(6Q26) WILD-TYPE  15  95 353  57
D41V5, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  T1                         5                          15
  T2                        10                          95
  T3                        64                         353
  T4                        12                          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 17(6Q26) MUTATED    42  18  30
  DEL PEAK 17(6Q26) WILD-TYPE 304 132  85
D41V6, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  N0                        42                         304
  N1                        18                         132
  N2                        30                          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"
D41V7, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    59  18
  DEL PEAK 17(6Q26) WILD-TYPE 394  70
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     59   18
  DEL PEAK 17(6Q26) WILD-TYPE  394   70
   clus
vv  DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  0                        59                         394
  1                        18                          70
[1] 2 2
[1] FALSE
D41V8, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    37  54
  DEL PEAK 17(6Q26) WILD-TYPE 252 271
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     37   54
  DEL PEAK 17(6Q26) WILD-TYPE  252  271
        clus
vv       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  FEMALE                        37                         252
  MALE                          54                         271
[1] 2 2
[1] FALSE
D41V9, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED    66   9
  DEL PEAK 17(6Q26) WILD-TYPE 416  20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED     66    9
  DEL PEAK 17(6Q26) WILD-TYPE  416   20
     clus
vv    DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  NO                         66                         416
  YES                         9                          20
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK 17(6Q26) MUTATED                     52
  DEL PEAK 17(6Q26) WILD-TYPE                  330
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(6Q26) MUTATED                               8
  DEL PEAK 17(6Q26) WILD-TYPE                            54
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK 17(6Q26) MUTATED                      22
  DEL PEAK 17(6Q26) WILD-TYPE                   124
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 17(6Q26) MUTATED                                6
  DEL PEAK 17(6Q26) WILD-TYPE                              7
D41V10, multiclass
                                clus
vv                               DEL PEAK 17(6Q26) MUTATED
  COLON ADENOCARCINOMA                                  52
  COLON MUCINOUS ADENOCARCINOMA                          8
  RECTAL ADENOCARCINOMA                                 22
  RECTAL MUCINOUS ADENOCARCINOMA                         6
                                clus
vv                               DEL PEAK 17(6Q26) WILD-TYPE
  COLON ADENOCARCINOMA                                   330
  COLON MUCINOUS ADENOCARCINOMA                           54
  RECTAL ADENOCARCINOMA                                  124
  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"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 17(6Q26) MUTATED    61   1   8   7
  DEL PEAK 17(6Q26) WILD-TYPE 385   5  29  22
D41V11, multiclass
    clus
vv   DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  R0                        61                         385
  R1                         1                           5
  R2                         8                          29
  RX                         7                          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"
D41V12, continuous
D41V13, binary
                             cls
clus                            0   1
  DEL PEAK 17(6Q26) MUTATED     0  45
  DEL PEAK 17(6Q26) WILD-TYPE   5 307
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 17(6Q26) MUTATED      0   45
  DEL PEAK 17(6Q26) WILD-TYPE    5  307
                        clus
vv                       DEL PEAK 17(6Q26) MUTATED DEL PEAK 17(6Q26) WILD-TYPE
  HISPANIC OR LATINO                             0                           5
  NOT HISPANIC OR LATINO                        45                         307
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 18(7Q31.1) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 18(7Q31.1) MUTATED    13   3
  DEL PEAK 18(7Q31.1) WILD-TYPE 453 125
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                           16                           578 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                            3                           125 
$`DEL PEAK 18(7Q31.1) MUTATED`
TCGA-AA-A00L TCGA-AD-6548 TCGA-5M-AAT4 TCGA-A6-3807 TCGA-AA-A01R TCGA-AU-3779 
       38.04        21.37         1.61        34.65        35.01        14.50 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-6170 TCGA-D5-6932 TCGA-DM-A0XD 
       29.06        22.03         5.03        15.02        11.38        24.43 
TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-A008 TCGA-DC-6682 
       34.03         6.05        13.94        25.05 

$`DEL PEAK 18(7Q31.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 
       58.03        13.02        24.03        37.05        36.03         8.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 
       19.07        34.03         0.99        13.02        17.95        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 
       19.99        19.99         6.05         0.92        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 
       85.05        19.04        19.04        14.93        31.07        24.03 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 
       29.98        12.99        24.00         2.01        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6888 TCGA-AD-6895 
       24.00        19.07        21.99        39.06        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       35.80        26.17        91.79        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 
       55.76        26.43        15.62         4.80        12.66         9.53 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
       39.45        43.76        46.65        43.76        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 
       25.08        25.18        20.61        21.76        24.69        24.39 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 
       23.87        20.12        19.66        20.28        16.24        24.92 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 
       61.84        56.25         9.63         5.03         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 
        1.02        37.05        35.01        63.98         6.97         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
       38.99         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       24.00        29.95        20.98        13.94        61.02        78.08 
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-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 
       47.01        15.02        11.01         5.98        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        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-3845 
       17.98        15.95        38.99        36.95        37.02         0.00 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
       17.03        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 
       32.05         0.99        31.07        53.00        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-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-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         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-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-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G 
       34.98        15.02        15.02        10.98        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07         1.02         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F 
        1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 
       22.42        27.42        26.47        16.44         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 
       27.09        16.31         0.95        33.01         0.20        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         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        25.02        26.04 
TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 
        8.02        27.02        13.02        22.98        30.08        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 
       15.02        15.02        15.02        17.03        15.02        12.00 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 
       14.04        29.03        16.04        21.99        14.99        12.99 
TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 
       13.02        14.04        11.01        12.95        13.05        11.08 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       11.08        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 
       18.25        25.48        43.27        15.12        17.85         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
       17.13        12.49        16.14        15.58         7.53        12.39 
TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 
       10.13        12.43        14.30         9.04         9.44        11.64 
TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XF 
       13.41        13.35        12.00        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-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 
      117.07        98.24        95.18         8.61        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
       15.65        12.79        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H 
        8.42        31.30        21.90        38.70        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02        46.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       35.01        14.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       19.99        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        20.98         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        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        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       10.98        44.02        25.97        25.05        12.62       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 
        3.48         4.18        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-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                         1.61                          0.00 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        38.04                        148.01 
  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE 
                        21.70                         22.01 
[1] "1.6 - 38.0 (21.7)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.3"
D42V2, continuous
D42V3, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED    13   4
  DEL PEAK 18(7Q31.1) WILD-TYPE 435 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     13    4
  DEL PEAK 18(7Q31.1) WILD-TYPE  435  158
        clus
vv       DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  COLON                           13                           435
  RECTUM                           4                           158
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 18(7Q31.1) MUTATED         3        0        0         7         0
  DEL PEAK 18(7Q31.1) WILD-TYPE     101        1       37       165        12
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 18(7Q31.1) MUTATED           0         1          1          1
  DEL PEAK 18(7Q31.1) WILD-TYPE         2        23         14         83
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 18(7Q31.1) MUTATED            2        1         1         0
  DEL PEAK 18(7Q31.1) WILD-TYPE         53       62        23         2
D42V4, multiclass
            clus
vv           DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  STAGE I                              3                           101
  STAGE IA                             0                             1
  STAGE II                             0                            37
  STAGE IIA                            7                           165
  STAGE IIB                            0                            12
  STAGE IIC                            0                             2
  STAGE III                            1                            23
  STAGE IIIA                           1                            14
  STAGE IIIB                           1                            83
  STAGE IIIC                           2                            53
  STAGE IV                             1                            62
  STAGE IVA                            1                            23
  STAGE IVB                            0                             2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 18(7Q31.1) MUTATED     0   4  13   0
  DEL PEAK 18(7Q31.1) WILD-TYPE  20 101 404  69
D42V5, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  T1                           0                            20
  T2                           4                           101
  T3                          13                           404
  T4                           0                            69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 18(7Q31.1) MUTATED    11   3   3
  DEL PEAK 18(7Q31.1) WILD-TYPE 335 147 112
D42V6, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  N0                          11                           335
  N1                           3                           147
  N2                           3                           112
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED    15   2
  DEL PEAK 18(7Q31.1) WILD-TYPE 438  86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     15    2
  DEL PEAK 18(7Q31.1) WILD-TYPE  438   86
   clus
vv  DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  0                          15                           438
  1                           2                            86
[1] 2 2
[1] FALSE
D42V8, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED     9   8
  DEL PEAK 18(7Q31.1) WILD-TYPE 280 317
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      9    8
  DEL PEAK 18(7Q31.1) WILD-TYPE  280  317
        clus
vv       DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  FEMALE                           9                           280
  MALE                             8                           317
[1] 2 2
[1] FALSE
D42V9, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED    12   3
  DEL PEAK 18(7Q31.1) WILD-TYPE 470  26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED     12    3
  DEL PEAK 18(7Q31.1) WILD-TYPE  470   26
     clus
vv    DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  NO                           12                           470
  YES                           3                            26
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 18(7Q31.1) MUTATED                     12
  DEL PEAK 18(7Q31.1) WILD-TYPE                  370
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(7Q31.1) MUTATED                               1
  DEL PEAK 18(7Q31.1) WILD-TYPE                            61
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 18(7Q31.1) MUTATED                       3
  DEL PEAK 18(7Q31.1) WILD-TYPE                   143
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 18(7Q31.1) MUTATED                                1
  DEL PEAK 18(7Q31.1) WILD-TYPE                             12
D42V10, multiclass
                                clus
vv                               DEL PEAK 18(7Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    12
  COLON MUCINOUS ADENOCARCINOMA                            1
  RECTAL ADENOCARCINOMA                                    3
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 18(7Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     370
  COLON MUCINOUS ADENOCARCINOMA                             61
  RECTAL ADENOCARCINOMA                                    143
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 18(7Q31.1) MUTATED    16   0   0   0
  DEL PEAK 18(7Q31.1) WILD-TYPE 430   6  37  29
D42V11, multiclass
    clus
vv   DEL PEAK 18(7Q31.1) MUTATED DEL PEAK 18(7Q31.1) WILD-TYPE
  R0                          16                           430
  R1                           0                             6
  R2                           0                            37
  RX                           0                            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"
D42V12, continuous
D42V13, binary
                               cls
clus                              0   1
  DEL PEAK 18(7Q31.1) MUTATED     2   9
  DEL PEAK 18(7Q31.1) WILD-TYPE   3 343
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 18(7Q31.1) MUTATED      2    9
  DEL PEAK 18(7Q31.1) WILD-TYPE    3  343
                        clus
vv                       DEL PEAK 18(7Q31.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       DEL PEAK 18(7Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           343
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 19(8P23.2) MUTATION ANALYSIS
D43V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 19(8P23.2) MUTATED   213  67
  DEL PEAK 19(8P23.2) WILD-TYPE 253  61
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                          280                           314 
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                           67                            61 
$`DEL PEAK 19(8P23.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3543 
       24.33        45.60         1.02        24.03        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 
       13.02        23.01        19.99        19.99         6.05        19.00 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3952 
       36.00        85.05        31.07        24.03        29.98         2.01 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 
       26.01        24.00        15.52       106.75         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6586 TCGA-G4-6625 TCGA-AF-3913 
        5.88        23.51        35.93        35.80        91.79        10.39 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       13.94        19.99        17.03        17.03        25.97        15.95 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-4N-A93T 
       31.00        51.98        21.24        18.28        26.43         4.80 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 
        1.61         9.53        43.76        43.76        43.43        42.28 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 
       44.91        35.11        16.57        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        56.25         9.63         5.03         1.02        37.05 
TCGA-AA-3517 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       38.99         0.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 
       33.99        21.01        24.00        78.08         2.01        14.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3842 TCGA-AA-3851 
       47.01        15.02         5.98        37.05        37.02        33.07 
TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3930 
       36.03         0.99        31.07        17.03        27.02         2.01 
TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D 
       34.03        16.08        34.06        27.02         7.96        19.00 
TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S 
       34.03        17.03        15.02        12.00        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02W 
       33.04        37.02         2.96        39.98         5.03        41.00 
TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-5543 
       40.96         5.79        22.42        26.47        16.31        33.01 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4684 
        0.20        17.85        18.84       109.28         5.65        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-CA-5797 TCGA-CA-6715 TCGA-CA-6719 TCGA-CK-4952 TCGA-CM-4751 TCGA-CM-4752 
       12.59        12.59        14.30        15.62        27.02        13.02 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 
       22.03        22.98        30.08        32.02         5.03        17.03 
TCGA-CM-6163 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 
       14.04        21.99        13.02        15.02        13.05        11.08 
TCGA-CM-6679 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 
       10.06        54.61        56.09        55.92        17.75        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       43.27        15.12        12.49        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.43         9.04        13.41        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28A 
      130.65        49.91        13.32       140.38       131.51        26.47 
TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6463 TCGA-F4-6704 
       35.97        60.79       117.07        31.96        35.74         1.55 
TCGA-F4-6805 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 
       34.42         0.53         8.35        74.56        65.85        44.68 
TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-NH-A50U TCGA-NH-A50V 
       39.42        61.91        36.00        26.43        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
        9.93        15.65        16.80         8.42        21.90        38.70 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 
       37.74        24.36        20.02        24.59        65.98        32.02 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
       34.03         2.01         6.05         0.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3893 
       29.98        32.98         0.99        19.04         1.02        35.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J 
        1.02         3.98        20.98        23.01         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 
        1.02         1.94        38.96        41.00         2.50        27.55 
TCGA-CI-6621 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
       13.78        48.20        78.12        21.01        25.05        31.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       13.97        31.00        51.98        10.98        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 
       12.62       126.44        41.36        57.24       129.27         3.48 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        4.18        15.85        16.34        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         9.96        42.35        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        11.87        12.46 

$`DEL PEAK 19(8P23.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 
       13.94        14.53        24.16        58.03        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 
       36.03         8.05        19.07        17.95         0.92        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3986 
       19.04        14.93        12.99        24.00        50.99        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6588 
       75.95       100.01        28.21        63.62        22.09        26.17 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-A015 TCGA-G5-6235 TCGA-3L-AA1B 
       79.69        17.85         8.02        36.03        55.76        15.62 
TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 
       12.66        39.45        46.65        42.90        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       37.02        32.75        32.45        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6651 TCGA-A6-6653 
       22.06        32.71        22.52         8.38        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         7.04         3.02 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         6.97         1.02         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       19.07        29.00        29.95        20.98        13.94        61.02 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 
        6.97        54.02        50.04        47.05        11.01         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        36.95         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 
       10.06         0.00         0.00        32.05        53.00        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 
       31.00        24.00        33.01        26.01        20.98         2.01 
TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       21.99        13.05        25.02        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       30.02        18.05        18.05         4.01        27.02        42.02 
TCGA-AA-A00R TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
        0.99        14.99        34.98        15.02        10.98        32.02 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X 
       31.00        38.07         1.02        35.01         1.02        26.01 
TCGA-AA-A029 TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       51.98         2.01         0.92        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       12.16        83.24        24.53        27.42        16.44         0.46 
TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 
        0.92        14.50        27.09         0.95        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       17.26        19.33        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5254 TCGA-CA-5255 
       22.36        88.21        49.41         6.77        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.46        12.39        12.20        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
      148.01        85.45        70.16        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         2.01       124.27        23.05        20.02        37.02 
TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5861 TCGA-CM-5863 
       25.02        26.04         8.02        29.06        15.02        15.02 
TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6167 
       15.02        15.02        12.00        29.03        16.04        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-D5-5537 TCGA-D5-5539 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       12.03        45.40        19.59        20.19        20.42        18.25 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 
       17.85         4.80        17.13        16.14        12.39        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 
       92.75        12.59         7.50        44.32       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-F4-6459 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 
        8.61        11.11        35.74         6.18        47.87        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       43.04        33.67        13.25        47.41        35.31       133.18 
TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6322 
       82.39        67.30        53.62        55.04        85.48        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GC 
       13.78        46.75        74.79        18.18        19.33        12.79 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H 
       42.77        29.46        32.98        31.30        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56N 
       70.03        46.92        29.98        16.83        86.63        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3599 
       36.03        12.00         7.07        20.05        50.04        12.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 
       15.95        19.99        20.98        37.02         0.99        19.99 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       17.95        36.95        13.02        14.01        48.03        25.02 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A025 TCGA-AG-A02N 
       46.03        13.94         6.02        37.02        49.97        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       38.04        38.56        43.20        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 
       33.17        44.78        47.44         7.17        26.04        12.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       44.02        25.97        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6814 
       16.41         8.61        17.46        49.51        32.19        37.18 
TCGA-F5-6861 TCGA-G5-6572 
       38.14        47.08 

  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                            0                             0 
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                       140.38                        148.01 
  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE 
                       23.260                        21.405 
[1] "0.0 - 140.4 (23.3)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.4"
D43V2, continuous
D43V3, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.2) MUTATED   188  98
  DEL PEAK 19(8P23.2) WILD-TYPE 260  64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.2) MUTATED    188   98
  DEL PEAK 19(8P23.2) WILD-TYPE  260   64
        clus
vv       DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  COLON                          188                           260
  RECTUM                          98                            64
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 19(8P23.2) MUTATED        40        0       13        62         3
  DEL PEAK 19(8P23.2) WILD-TYPE      64        1       24       110         9
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 19(8P23.2) MUTATED           1        11          8         45
  DEL PEAK 19(8P23.2) WILD-TYPE         1        13          7         39
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 19(8P23.2) MUTATED           34       46        13         1
  DEL PEAK 19(8P23.2) WILD-TYPE         21       17        11         1
D43V4, multiclass
            clus
vv           DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  STAGE I                             40                            64
  STAGE IA                             0                             1
  STAGE II                            13                            24
  STAGE IIA                           62                           110
  STAGE IIB                            3                             9
  STAGE IIC                            1                             1
  STAGE III                           11                            13
  STAGE IIIA                           8                             7
  STAGE IIIB                          45                            39
  STAGE IIIC                          34                            21
  STAGE IV                            46                            17
  STAGE IVA                           13                            11
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 19(8P23.2) MUTATED     4  47 202  34
  DEL PEAK 19(8P23.2) WILD-TYPE  16  58 215  35
D43V5, multiclass
    clus
vv   DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  T1                           4                            16
  T2                          47                            58
  T3                         202                           215
  T4                          34                            35
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             N0  N1  N2
  DEL PEAK 19(8P23.2) MUTATED   132  81  73
  DEL PEAK 19(8P23.2) WILD-TYPE 214  69  42
D43V6, multiclass
    clus
vv   DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  N0                         132                           214
  N1                          81                            69
  N2                          73                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.2) MUTATED   197  59
  DEL PEAK 19(8P23.2) WILD-TYPE 256  29
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.2) MUTATED    197   59
  DEL PEAK 19(8P23.2) WILD-TYPE  256   29
   clus
vv  DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  0                         197                           256
  1                          59                            29
[1] 2 2
[1] FALSE
D43V8, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.2) MUTATED   122 166
  DEL PEAK 19(8P23.2) WILD-TYPE 167 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.2) MUTATED    122  166
  DEL PEAK 19(8P23.2) WILD-TYPE  167  159
        clus
vv       DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  FEMALE                         122                           167
  MALE                           166                           159
[1] 2 2
[1] FALSE
D43V9, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.2) MUTATED   222  14
  DEL PEAK 19(8P23.2) WILD-TYPE 260  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.2) MUTATED    222   14
  DEL PEAK 19(8P23.2) WILD-TYPE  260   15
     clus
vv    DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  NO                          222                           260
  YES                          14                            15
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 19(8P23.2) MUTATED                    170
  DEL PEAK 19(8P23.2) WILD-TYPE                  212
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(8P23.2) MUTATED                              15
  DEL PEAK 19(8P23.2) WILD-TYPE                            47
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 19(8P23.2) MUTATED                      89
  DEL PEAK 19(8P23.2) WILD-TYPE                    57
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 19(8P23.2) MUTATED                                7
  DEL PEAK 19(8P23.2) WILD-TYPE                              6
D43V10, multiclass
                                clus
vv                               DEL PEAK 19(8P23.2) MUTATED
  COLON ADENOCARCINOMA                                   170
  COLON MUCINOUS ADENOCARCINOMA                           15
  RECTAL ADENOCARCINOMA                                   89
  RECTAL MUCINOUS ADENOCARCINOMA                           7
                                clus
vv                               DEL PEAK 19(8P23.2) WILD-TYPE
  COLON ADENOCARCINOMA                                     212
  COLON MUCINOUS ADENOCARCINOMA                             47
  RECTAL ADENOCARCINOMA                                     57
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 19(8P23.2) MUTATED   199   3  26   9
  DEL PEAK 19(8P23.2) WILD-TYPE 247   3  11  20
D43V11, multiclass
    clus
vv   DEL PEAK 19(8P23.2) MUTATED DEL PEAK 19(8P23.2) WILD-TYPE
  R0                         199                           247
  R1                           3                             3
  R2                          26                            11
  RX                           9                            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
D43V13, binary
                               cls
clus                              0   1
  DEL PEAK 19(8P23.2) MUTATED     4 163
  DEL PEAK 19(8P23.2) WILD-TYPE   1 189
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 19(8P23.2) MUTATED      4  163
  DEL PEAK 19(8P23.2) WILD-TYPE    1  189
                        clus
vv                       DEL PEAK 19(8P23.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         163
                        clus
vv                       DEL PEAK 19(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           189
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 20(8P22) MUTATION ANALYSIS
D44V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 20(8P22) MUTATED   219  74
  DEL PEAK 20(8P22) WILD-TYPE 247  54
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                        293                         301 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                         74                          54 
$`DEL PEAK 20(8P22) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3496 TCGA-AA-3520 TCGA-AA-3531 TCGA-AA-3552 
       24.33        45.60         1.02        24.03        34.03        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 
       23.01        19.99        19.99         6.05        19.00        36.00 
TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3976 TCGA-AA-3979 
       85.05        31.07        24.03        29.98        26.01        24.00 
TCGA-AA-A00L TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       38.04        15.52       106.75         1.94        49.08         5.88 
TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6586 TCGA-G4-6625 TCGA-AF-3913 TCGA-AG-3611 
       23.51        35.93        35.80        91.79        10.39        13.94 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        25.97        15.95        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AAT6 
       21.24        18.28        26.43         4.80         1.61         9.53 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.76        43.43        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 
       16.57        34.65        36.53        32.91        31.63        30.44 
TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6142 
       29.19        23.61        29.16        27.09        24.13        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 
       25.18        20.61        24.69        23.87        20.28        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3517 
       56.25         9.63         5.03         1.02        37.05        38.99 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3660 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 
       21.01        24.00        78.08        54.02         2.01        14.01 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3842 
       47.01        15.02        11.01         5.98        37.05        37.02 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       10.06        33.07        36.03         0.99        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3930 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 
       27.02         2.01        34.03        16.08        34.06        27.02 
TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00U TCGA-AA-A017 TCGA-AA-A01G 
        7.96        19.00        34.03        17.03        15.02        12.00 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02J 
       31.00         1.02        33.04        37.02         2.96         5.03 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AM-5820 
       41.00        40.96         5.79        22.42        26.47         0.46 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       16.31        33.01         0.20        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 
      109.28         5.65        22.36        65.00        62.79        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5797 TCGA-CA-6715 
       29.56         5.23        11.74         3.19        12.59        12.59 
TCGA-CA-6719 TCGA-CK-4948 TCGA-CK-4952 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
       14.30       148.01        15.62        27.02        13.02        22.03 
TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6163 
       22.98        30.08        32.02         5.03        17.03        14.04 
TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 
       21.99        13.02        15.02        11.01        13.05        11.08 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6533 
       54.61        19.59        56.09        55.92        17.75        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 
       43.27        15.12        12.49        15.58         7.53        10.13 
TCGA-D5-6923 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF 
       12.43         9.04        13.41        11.38        24.43        38.20 
TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA 
      130.65        49.91        13.32       140.38        44.32       131.51 
TCGA-DM-A28A TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-F4-6459 TCGA-F4-6460 
       26.47        35.97        60.79       117.07         8.61        31.96 
TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6854 
       11.11        35.74         1.55        34.42        13.25         0.53 
TCGA-G4-6295 TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6311 TCGA-G4-6315 
        8.35        74.56        65.85        44.68        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V 
       36.00        26.43        26.04        46.75        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
        9.93        15.65        16.80         8.42        21.90        38.70 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       34.49        37.74        24.36        20.02        24.59        65.98 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       32.02        36.03        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 
       34.03        34.03         2.01         6.05         0.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 
        0.99        29.98        32.98         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       17.95        35.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A011 
       36.03        14.04         1.02         3.98        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
        9.07         1.02         1.02         1.94        38.96        41.00 
TCGA-AH-6547 TCGA-AH-6644 TCGA-CI-6621 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 
        2.50        27.55        13.78        48.20        78.12        21.01 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       25.05        31.00        13.97        31.00        51.98        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6883 
      129.27         3.48         4.18        15.85        16.34        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       10.78        13.64        11.97         8.45         9.96        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
       28.57         0.39        19.66        11.87        12.46 

$`DEL PEAK 20(8P22) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 
       13.94        14.53        24.16        58.03        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 
       36.03         8.05        19.07         0.99        17.95         0.92 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       19.04        19.04        14.93        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3986 TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       50.99        19.07        21.99        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6321 
       10.88        75.95       100.01        28.21        63.62        22.09 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-A015 
       26.17        79.69        17.85         8.02        19.99        36.03 
TCGA-G5-6235 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2676 
       55.76        15.62        12.66        39.45        46.65        42.90 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5661 
       37.05        37.25        37.02        32.75        32.45        33.53 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6651 
       22.09        22.06        32.71        22.52         8.38        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         7.04 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 
        3.02        35.01        63.98         6.97         1.02         1.02 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3534 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
        9.07        19.07        29.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3696 TCGA-AA-3710 
       61.02         6.97        50.04        47.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 
       15.95        38.99        36.95         0.00        17.03         0.00 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3941 
        0.00        32.05        53.00        18.05        31.00        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 
       33.01        26.01        20.98         2.01        21.99        13.05 
TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
       25.02        27.02        13.94        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00W 
       18.05         4.01        27.02        42.02         0.99        14.99 
TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01I TCGA-AA-A01P 
       34.98        15.02        10.98        32.02        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02F 
        1.02        35.01         1.02        26.01        51.98        39.98 
TCGA-AA-A02H TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        2.01         0.92        22.03        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5821 TCGA-AU-3779 
       83.24        24.53        27.42        16.44         0.92        14.50 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AZ-4315 
       27.09         0.95        21.44        17.82        17.26        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        88.21        49.41         6.77 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6716 TCGA-CA-6717 
       12.69        12.36        12.46        12.39        12.20        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-5913 TCGA-CK-5914 
       10.06        17.56        85.45        70.16        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5861 
       37.02        25.02        26.04         8.02        29.06        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6164 TCGA-CM-6165 
       15.02        15.02        15.02        12.00        29.03        16.04 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 
       14.99        12.99        14.04        12.95        11.08        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       10.06        12.03        45.40        20.19        20.42        18.25 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6924 
       17.85         4.80        17.13        16.14        12.39        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 
        9.44        11.64        13.35        12.00        10.26       119.70 
TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       92.75        12.59         7.50       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6569 
       14.04        81.37       119.93        98.24        95.18        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6855 
        6.18        47.87        41.42        43.04        33.67        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6307 
       35.31       133.18        82.39        67.30        53.62        55.04 
TCGA-G4-6309 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GC 
       85.48        13.78        74.79        18.18        19.33        12.79 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-T9-A92H 
       42.77        29.46        32.98        31.30        60.13        11.90 
TCGA-WS-AB45 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       70.03        29.98        16.83        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 
       12.00         7.07        20.05        50.04        12.03        15.95 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       19.99        20.98        37.02         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-4022 TCGA-AG-A002 
       13.02        14.01        48.03        25.02        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       13.94         6.02        49.97        61.97        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       43.20        26.43        19.46         6.05        33.17        44.78 
TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 
       47.44         7.17        26.04        12.00        44.02        25.97 
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        49.51        32.19        36.49        37.18        38.14 
TCGA-G5-6572 
       47.08 

  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                          0                           0 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                     148.01                      139.17 
  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE 
                      23.51                       21.14 
[1] "0.0 - 148.0 (23.5)" "0.0 - 139.2 (21.1)"
[1] "hr=" "1.5"
D44V2, continuous
D44V3, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED   201  99
  DEL PEAK 20(8P22) WILD-TYPE 247  63
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED    201   99
  DEL PEAK 20(8P22) WILD-TYPE  247   63
        clus
vv       DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  COLON                        201                         247
  RECTUM                        99                          63
[1] 2 2
[1] FALSE
                             vv
clus                          STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 20(8P22) MUTATED        40        0       14        64         3
  DEL PEAK 20(8P22) WILD-TYPE      64        1       23       108         9
                             vv
clus                          STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 20(8P22) MUTATED           1        12          9         48
  DEL PEAK 20(8P22) WILD-TYPE         1        12          6         36
                             vv
clus                          STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 20(8P22) MUTATED           37       46        16         1
  DEL PEAK 20(8P22) WILD-TYPE         18       17         8         1
D44V4, multiclass
            clus
vv           DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  STAGE I                           40                          64
  STAGE IA                           0                           1
  STAGE II                          14                          23
  STAGE IIA                         64                         108
  STAGE IIB                          3                           9
  STAGE IIC                          1                           1
  STAGE III                         12                          12
  STAGE IIIA                         9                           6
  STAGE IIIB                        48                          36
  STAGE IIIC                        37                          18
  STAGE IV                          46                          17
  STAGE IVA                         16                           8
  STAGE IVB                          1                           1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  DEL PEAK 20(8P22) MUTATED     4  47 213  37
  DEL PEAK 20(8P22) WILD-TYPE  16  58 204  32
D44V5, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  T1                         4                          16
  T2                        47                          58
  T3                       213                         204
  T4                        37                          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 20(8P22) MUTATED   136  85  79
  DEL PEAK 20(8P22) WILD-TYPE 210  65  36
D44V6, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  N0                       136                         210
  N1                        85                          65
  N2                        79                          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"
D44V7, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED   207  62
  DEL PEAK 20(8P22) WILD-TYPE 246  26
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED    207   62
  DEL PEAK 20(8P22) WILD-TYPE  246   26
   clus
vv  DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  0                       207                         246
  1                        62                          26
[1] 2 2
[1] FALSE
D44V8, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED   132 170
  DEL PEAK 20(8P22) WILD-TYPE 157 155
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED    132  170
  DEL PEAK 20(8P22) WILD-TYPE  157  155
        clus
vv       DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  FEMALE                       132                         157
  MALE                         170                         155
[1] 2 2
[1] FALSE
D44V9, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED   232  16
  DEL PEAK 20(8P22) WILD-TYPE 250  13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED    232   16
  DEL PEAK 20(8P22) WILD-TYPE  250   13
     clus
vv    DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  NO                        232                         250
  YES                        16                          13
[1] 2 2
[1] FALSE
                             vv
clus                          COLON ADENOCARCINOMA
  DEL PEAK 20(8P22) MUTATED                    182
  DEL PEAK 20(8P22) WILD-TYPE                  200
                             vv
clus                          COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(8P22) MUTATED                              16
  DEL PEAK 20(8P22) WILD-TYPE                            46
                             vv
clus                          RECTAL ADENOCARCINOMA
  DEL PEAK 20(8P22) MUTATED                      90
  DEL PEAK 20(8P22) WILD-TYPE                    56
                             vv
clus                          RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 20(8P22) MUTATED                                7
  DEL PEAK 20(8P22) WILD-TYPE                              6
D44V10, multiclass
                                clus
vv                               DEL PEAK 20(8P22) MUTATED
  COLON ADENOCARCINOMA                                 182
  COLON MUCINOUS ADENOCARCINOMA                         16
  RECTAL ADENOCARCINOMA                                 90
  RECTAL MUCINOUS ADENOCARCINOMA                         7
                                clus
vv                               DEL PEAK 20(8P22) WILD-TYPE
  COLON ADENOCARCINOMA                                   200
  COLON MUCINOUS ADENOCARCINOMA                           46
  RECTAL ADENOCARCINOMA                                   56
  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"
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 20(8P22) MUTATED   212   3  26   9
  DEL PEAK 20(8P22) WILD-TYPE 234   3  11  20
D44V11, multiclass
    clus
vv   DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  R0                       212                         234
  R1                         3                           3
  R2                        26                          11
  RX                         9                          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"
D44V12, continuous
D44V13, binary
                             cls
clus                            0   1
  DEL PEAK 20(8P22) MUTATED     4 175
  DEL PEAK 20(8P22) WILD-TYPE   1 177
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 20(8P22) MUTATED      4  175
  DEL PEAK 20(8P22) WILD-TYPE    1  177
                        clus
vv                       DEL PEAK 20(8P22) MUTATED DEL PEAK 20(8P22) WILD-TYPE
  HISPANIC OR LATINO                             4                           1
  NOT HISPANIC OR LATINO                       175                         177
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 21(8Q11.1) MUTATION ANALYSIS
D45V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 21(8Q11.1) MUTATED    34  12
  DEL PEAK 21(8Q11.1) WILD-TYPE 432 116
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           46                           548 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                           12                           116 
$`DEL PEAK 21(8Q11.1) MUTATED`
TCGA-A6-2677 TCGA-AA-3531 TCGA-G4-6298 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-3890 
       24.33        34.03        23.51        91.79        13.94        17.03 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-6650 TCGA-A6-6654 
       42.28        44.91        16.57        36.53        20.61        23.87 
TCGA-AA-3517 TCGA-AA-3544 TCGA-AA-3666 TCGA-AA-3681 TCGA-AA-3842 TCGA-AA-3989 
       38.99        14.01         2.01         5.98        37.02         7.96 
TCGA-AA-A01D TCGA-AA-A01K TCGA-AA-A02F TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK 
       10.98        31.00        39.98         0.20        17.85        18.84 
TCGA-CM-4746 TCGA-CM-5868 TCGA-CM-6675 TCGA-D5-5540 TCGA-D5-6531 TCGA-DM-A1D6 
       37.02        17.03        13.05        56.09        17.75        49.91 
TCGA-DM-A1HA TCGA-F4-6704 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3582 
      131.51         1.55        39.48        13.55        34.49        36.03 
TCGA-AG-3728 TCGA-AG-3909 TCGA-AG-A02G TCGA-AG-A02X TCGA-DC-6155 TCGA-DC-6156 
       29.98        19.99        38.96        41.00        13.97        31.00 
TCGA-DY-A1DG TCGA-EI-6513 TCGA-F5-6810 TCGA-F5-6813 
       51.48        16.34         0.39        19.66 

$`DEL PEAK 21(8Q11.1) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
        0.99        13.02        17.95        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 
        6.05         0.92        19.00        36.00        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 
       19.04        14.93        31.07        24.03        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       24.00         2.01        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 
       26.17        79.69        17.85        10.39         8.02        19.99 
TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        25.97        15.95        36.03        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 
       12.66         1.61         9.53        39.45        43.76        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 
       43.76        43.43        42.90        35.11        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        32.75        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        25.18        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        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         6.97         1.02         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 
       61.02        78.08         6.97        54.02        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 
       47.05        47.01        15.02        11.01        37.05         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 
       17.98        15.95        38.99        36.95         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       25.02        27.02        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-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         1.02        26.01        37.02 
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-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-4071 
        0.46         0.92        14.50        27.09        16.31         0.95 
TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 
       33.01        21.44        17.82        17.26        19.33       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 
       12.46        12.39        12.59        12.59        12.20        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         2.01 
TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4750 
      124.27        23.05        20.02        25.02        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-6161 
       32.02        15.02         5.03        15.02        15.02        15.02 
TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       12.00        14.04        29.03        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       12.99        13.02        15.02        14.04        11.01        12.95 
TCGA-CM-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        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       54.61        19.59        55.92        20.19        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       25.48        43.27        15.12        17.85         4.80        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 
       12.49        16.14        15.58         7.53        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 
       12.43        14.30         9.04         9.44        11.64        13.41 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       13.35        12.00        11.38        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 
       38.20       130.65        92.75        13.32        12.59       140.38 
TCGA-DM-A1DA TCGA-DM-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-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        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       35.74         6.18        47.87        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       33.67        13.25         0.53        47.41        35.31       133.18 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
        8.35        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 
       44.68        55.04        85.48        39.42        61.91        36.00 
TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       26.43        26.04        13.78        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC 
       10.98        19.33        19.33         9.93        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       16.80        42.77        29.46        32.98         8.42        31.30 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       21.90        38.70        60.13        11.90        70.03        46.92 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       17.23        43.04        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00        32.02         7.07        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
        9.07         1.02         1.02        49.97         1.94        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       19.46         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       31.00        12.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        32.61         3.48         4.18        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-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-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       28.57        32.19        36.49        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                          0.2                           0.0 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                       131.51                        148.01 
  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE 
                        23.69                         21.99 
[1] "0.2 - 131.5 (23.7)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D45V2, continuous
D45V3, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    30  16
  DEL PEAK 21(8Q11.1) WILD-TYPE 418 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     30   16
  DEL PEAK 21(8Q11.1) WILD-TYPE  418  146
        clus
vv       DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  COLON                           30                           418
  RECTUM                          16                           146
[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        12         1
  DEL PEAK 21(8Q11.1) WILD-TYPE     100        1       37       160        11
                               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         2        22         13         77
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 21(8Q11.1) MUTATED            7        6         4         1
  DEL PEAK 21(8Q11.1) WILD-TYPE         48       57        20         1
D45V4, multiclass
            clus
vv           DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  STAGE I                              4                           100
  STAGE IA                             0                             1
  STAGE II                             0                            37
  STAGE IIA                           12                           160
  STAGE IIB                            1                            11
  STAGE IIC                            0                             2
  STAGE III                            2                            22
  STAGE IIIA                           2                            13
  STAGE IIIB                           7                            77
  STAGE IIIC                           7                            48
  STAGE IV                             6                            57
  STAGE IVA                            4                            20
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 21(8Q11.1) MUTATED     0   7  34   5
  DEL PEAK 21(8Q11.1) WILD-TYPE  20  98 383  64
D45V5, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  T1                           0                            20
  T2                           7                            98
  T3                          34                           383
  T4                           5                            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"
                               vv
clus                             N0  N1  N2
  DEL PEAK 21(8Q11.1) MUTATED    18  16  12
  DEL PEAK 21(8Q11.1) WILD-TYPE 328 134 103
D45V6, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  N0                          18                           328
  N1                          16                           134
  N2                          12                           103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    31  11
  DEL PEAK 21(8Q11.1) WILD-TYPE 422  77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     31   11
  DEL PEAK 21(8Q11.1) WILD-TYPE  422   77
   clus
vv  DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  0                          31                           422
  1                          11                            77
[1] 2 2
[1] FALSE
D45V8, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    18  29
  DEL PEAK 21(8Q11.1) WILD-TYPE 271 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     18   29
  DEL PEAK 21(8Q11.1) WILD-TYPE  271  296
        clus
vv       DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  FEMALE                          18                           271
  MALE                            29                           296
[1] 2 2
[1] FALSE
D45V9, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED    37   1
  DEL PEAK 21(8Q11.1) WILD-TYPE 445  28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED     37    1
  DEL PEAK 21(8Q11.1) WILD-TYPE  445   28
     clus
vv    DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  NO                           37                           445
  YES                           1                            28
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 21(8Q11.1) MUTATED                     26
  DEL PEAK 21(8Q11.1) WILD-TYPE                  356
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(8Q11.1) MUTATED                               4
  DEL PEAK 21(8Q11.1) WILD-TYPE                            58
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 21(8Q11.1) MUTATED                      15
  DEL PEAK 21(8Q11.1) WILD-TYPE                   131
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 21(8Q11.1) MUTATED                                1
  DEL PEAK 21(8Q11.1) WILD-TYPE                             12
D45V10, multiclass
                                clus
vv                               DEL PEAK 21(8Q11.1) MUTATED
  COLON ADENOCARCINOMA                                    26
  COLON MUCINOUS ADENOCARCINOMA                            4
  RECTAL ADENOCARCINOMA                                   15
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 21(8Q11.1) WILD-TYPE
  COLON ADENOCARCINOMA                                     356
  COLON MUCINOUS ADENOCARCINOMA                             58
  RECTAL ADENOCARCINOMA                                    131
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 21(8Q11.1) MUTATED    38   0   4   0
  DEL PEAK 21(8Q11.1) WILD-TYPE 408   6  33  29
D45V11, multiclass
    clus
vv   DEL PEAK 21(8Q11.1) MUTATED DEL PEAK 21(8Q11.1) WILD-TYPE
  R0                          38                           408
  R1                           0                             6
  R2                           4                            33
  RX                           0                            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"
D45V12, continuous
D45V13, binary
                               cls
clus                              0   1
  DEL PEAK 21(8Q11.1) MUTATED     0  29
  DEL PEAK 21(8Q11.1) WILD-TYPE   5 323
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(8Q11.1) MUTATED      0   29
  DEL PEAK 21(8Q11.1) WILD-TYPE    5  323
                        clus
vv                       DEL PEAK 21(8Q11.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          29
                        clus
vv                       DEL PEAK 21(8Q11.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           323
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 22(9P21.3) MUTATION ANALYSIS
D46V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 22(9P21.3) MUTATED    63  18
  DEL PEAK 22(9P21.3) WILD-TYPE 403 110
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           81                           513 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                           18                           110 
$`DEL PEAK 22(9P21.3) MUTATED`
TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3562 TCGA-AA-3697 TCGA-AA-3867 
       14.53        24.16        58.03        19.99        85.05        24.03 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AD-6888 TCGA-AZ-6608 TCGA-AG-A014 TCGA-AG-A01N 
       12.99        50.99        15.52         1.94        15.95        31.00 
TCGA-5M-AATE TCGA-A6-2675 TCGA-A6-3810 TCGA-A6-5667 TCGA-A6-6651 TCGA-A6-A567 
       39.45        43.43        36.53        29.16        21.76        61.84 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3538 TCGA-AA-3553 TCGA-AA-3685 TCGA-AA-3842 
        6.97        38.99        26.01        24.00        37.05        37.02 
TCGA-AA-3855 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-A004 TCGA-AA-A01F TCGA-AA-A01K 
       32.05        24.00        20.98        13.94        32.02        31.00 
TCGA-AA-A01S TCGA-AA-A03J TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-A69D TCGA-AZ-4614 
        1.02        40.96        26.47        16.31        17.85         5.65 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4750 
        5.23         3.19        12.69        12.59        12.20         8.02 
TCGA-CM-5348 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 
       22.98        13.02        15.02        13.05        11.08        11.01 
TCGA-CM-6679 TCGA-D5-6529 TCGA-D5-6534 TCGA-D5-6898 TCGA-DM-A0XF TCGA-DM-A288 
       10.06        20.19        43.27         7.53        38.20        14.04 
TCGA-F4-6808 TCGA-G4-6295 TCGA-G4-6297 TCGA-NH-A6GA TCGA-T9-A92H TCGA-AF-2687 
       33.67         8.35        82.39         9.93        11.90        46.92 
TCGA-AF-2692 TCGA-AF-A56L TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3731 
       13.55        65.98        20.05        34.03         6.05        37.02 
TCGA-AG-3882 TCGA-AG-4021 TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6544 TCGA-CI-6619 
       19.99         3.98         1.94        38.96        38.56         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A1DF 
       44.78        48.20        25.05        10.98        44.02        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6514 
       51.48         3.48        16.31 

$`DEL PEAK 22(9P21.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-AA-3496 TCGA-AA-3516 TCGA-AA-3520 
       24.33        45.60        13.94         1.02        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 
       13.02        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       19.00        36.00        19.04        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       29.98        24.00         2.01        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 
       38.04        21.99        39.06        21.37        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
       75.95       106.75       100.01        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 
       91.79        79.69        17.85        10.39         8.02        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A023 
       19.99        17.03        17.03        25.97        36.03        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
       12.66         1.61         9.53        43.76        46.65        43.76 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        34.65        32.75        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-A6-6137 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-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        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        56.25 
TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
        9.63         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       35.01        63.98         1.02         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        0.00        29.00        29.00        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       21.01        29.95        20.98        13.94        61.02        78.08 
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-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        36.03         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       53.00        17.03        27.02        18.05        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       33.01        26.01        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 
       13.05        34.06        25.02        27.02         7.96        27.02 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K 
       38.04        19.00        30.02        34.03        18.05        18.05 
TCGA-AA-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-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       34.98        15.02        15.02        10.98        12.00        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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       37.02        51.98         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        0.92        22.03        41.00        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
       83.24        24.53         5.79        22.42        27.42        16.44 
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        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
        0.20        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
      109.28        58.39         1.41        32.94         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       29.56        11.74        12.36        12.46        12.39        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
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        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 
       26.04        27.02        13.02        29.06        22.03        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 
       32.02        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-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       14.99        12.99        14.04        11.01        12.95        11.08 
TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 
       12.03        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        25.48        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
        4.80        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-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       13.41        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       24.43       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 
      140.38         7.50        44.32       131.51       135.65         7.76 
TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
      139.17        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        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        43.04        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
      133.18        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 
       55.04        85.48        39.42        61.91        36.00        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       26.04        13.78        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL 
       29.46        32.98         8.42        31.30        21.90        38.70 
TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 
       60.13        70.03        39.48        17.23        43.04        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.59        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        7.07        36.03        24.00         1.02        46.03        34.03 
TCGA-AG-3592 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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       19.99        20.98         7.99         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
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-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
        9.07         1.02         1.02        49.97        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       33.17        13.78        47.44        78.12         7.17        21.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       57.24       129.27        32.61         4.18        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-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        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                         1.02                          0.00 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                        85.05                        148.01 
  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE 
                        20.98                         22.03 
[1] "1.0 - 85.0 (21.0)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.2"
D46V2, continuous
D46V3, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    61  25
  DEL PEAK 22(9P21.3) WILD-TYPE 387 137
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     61   25
  DEL PEAK 22(9P21.3) WILD-TYPE  387  137
        clus
vv       DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  COLON                           61                           387
  RECTUM                          25                           137
[1] 2 2
[1] FALSE
                               vv
clus                            STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 22(9P21.3) MUTATED        16        0        5        20         2
  DEL PEAK 22(9P21.3) WILD-TYPE      88        1       32       152        10
                               vv
clus                            STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 22(9P21.3) MUTATED           0         2          3          9
  DEL PEAK 22(9P21.3) WILD-TYPE         2        22         12         75
                               vv
clus                            STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 22(9P21.3) MUTATED           11       12         4         1
  DEL PEAK 22(9P21.3) WILD-TYPE         44       51        20         1
D46V4, multiclass
            clus
vv           DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  STAGE I                             16                            88
  STAGE IA                             0                             1
  STAGE II                             5                            32
  STAGE IIA                           20                           152
  STAGE IIB                            2                            10
  STAGE IIC                            0                             2
  STAGE III                            2                            22
  STAGE IIIA                           3                            12
  STAGE IIIB                           9                            75
  STAGE IIIC                          11                            44
  STAGE IV                            12                            51
  STAGE IVA                            4                            20
  STAGE IVB                            1                             1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 22(9P21.3) MUTATED     2  20  53  12
  DEL PEAK 22(9P21.3) WILD-TYPE  18  85 364  57
D46V5, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  T1                           2                            18
  T2                          20                            85
  T3                          53                           364
  T4                          12                            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 22(9P21.3) MUTATED    44  23  20
  DEL PEAK 22(9P21.3) WILD-TYPE 302 127  95
D46V6, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  N0                          44                           302
  N1                          23                           127
  N2                          20                            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"
D46V7, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    64  18
  DEL PEAK 22(9P21.3) WILD-TYPE 389  70
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     64   18
  DEL PEAK 22(9P21.3) WILD-TYPE  389   70
   clus
vv  DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  0                          64                           389
  1                          18                            70
[1] 2 2
[1] FALSE
D46V8, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    33  54
  DEL PEAK 22(9P21.3) WILD-TYPE 256 271
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     33   54
  DEL PEAK 22(9P21.3) WILD-TYPE  256  271
        clus
vv       DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  FEMALE                          33                           256
  MALE                            54                           271
[1] 2 2
[1] FALSE
D46V9, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED    69   4
  DEL PEAK 22(9P21.3) WILD-TYPE 413  25
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED     69    4
  DEL PEAK 22(9P21.3) WILD-TYPE  413   25
     clus
vv    DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  NO                           69                           413
  YES                           4                            25
[1] 2 2
[1] FALSE
                               vv
clus                            COLON ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                     58
  DEL PEAK 22(9P21.3) WILD-TYPE                  324
                               vv
clus                            COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                               2
  DEL PEAK 22(9P21.3) WILD-TYPE                            60
                               vv
clus                            RECTAL ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                      24
  DEL PEAK 22(9P21.3) WILD-TYPE                   122
                               vv
clus                            RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 22(9P21.3) MUTATED                                1
  DEL PEAK 22(9P21.3) WILD-TYPE                             12
D46V10, multiclass
                                clus
vv                               DEL PEAK 22(9P21.3) MUTATED
  COLON ADENOCARCINOMA                                    58
  COLON MUCINOUS ADENOCARCINOMA                            2
  RECTAL ADENOCARCINOMA                                   24
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 22(9P21.3) WILD-TYPE
  COLON ADENOCARCINOMA                                     324
  COLON MUCINOUS ADENOCARCINOMA                             60
  RECTAL ADENOCARCINOMA                                    122
  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"
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 22(9P21.3) MUTATED    55   3   8   4
  DEL PEAK 22(9P21.3) WILD-TYPE 391   3  29  25
D46V11, multiclass
    clus
vv   DEL PEAK 22(9P21.3) MUTATED DEL PEAK 22(9P21.3) WILD-TYPE
  R0                          55                           391
  R1                           3                             3
  R2                           8                            29
  RX                           4                            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"
D46V12, continuous
D46V13, binary
                               cls
clus                              0   1
  DEL PEAK 22(9P21.3) MUTATED     2  48
  DEL PEAK 22(9P21.3) WILD-TYPE   3 304
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 22(9P21.3) MUTATED      2   48
  DEL PEAK 22(9P21.3) WILD-TYPE    3  304
                        clus
vv                       DEL PEAK 22(9P21.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          48
                        clus
vv                       DEL PEAK 22(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           304
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 23(10P15.3) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(10P15.3) MUTATED    92  19
  DEL PEAK 23(10P15.3) WILD-TYPE 374 109
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                           111                            483 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                            19                            109 
$`DEL PEAK 23(10P15.3) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3692 TCGA-AA-3697 
       24.33        45.60        13.02        19.99        36.00        85.05 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-AA-A00Z TCGA-G4-6314 
       24.03         2.01        50.99        24.00        21.99        35.93 
TCGA-AG-A00H TCGA-G5-6641 TCGA-A6-2674 TCGA-A6-2680 TCGA-A6-5659 TCGA-A6-5666 
       25.97        26.43        43.76        35.11        30.44        32.71 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A5ZU 
       29.16        22.52        25.18        23.87        61.84         9.63 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3848 
        1.02         6.97        54.02        50.04        37.05        10.06 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00Q 
       31.07        17.03         7.96        34.03        18.05        42.02 
TCGA-AA-A01D TCGA-AA-A01X TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-A5EK TCGA-AM-5820 
       10.98        26.01        41.00        22.42        16.44         0.46 
TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4684 
       14.50         0.20         1.41         5.65         5.13        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        12.59        12.20        14.30 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 
        8.02        29.06        22.03        15.02        15.02        29.03 
TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-D5-6531 TCGA-D5-6535 
       13.02        15.02        11.08        11.08        17.75        15.12 
TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-G4-6297 TCGA-G4-6303 
        7.53        10.13         9.04        13.41        82.39        65.85 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A6GC TCGA-RU-A8FL 
       55.04        61.91        26.04        46.75        12.79        38.70 
TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56L 
       60.13        46.92        13.55        34.49        24.59        65.98 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3883 
       46.03        34.03        34.03        19.99         7.99         1.02 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A02X 
        1.02        19.99        28.04        13.94        23.01        41.00 
TCGA-AH-6544 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       38.56        48.20        25.05        13.97        31.00        51.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-6509 TCGA-EI-6514 
       25.05        25.05        57.24       129.27        17.00        16.31 
TCGA-EI-6881 TCGA-EI-7004 TCGA-F5-6702 
       16.41         8.45        28.57 

$`DEL PEAK 23(10P15.3) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3672 
        0.99        17.95        23.01        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       19.00        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
       12.99        24.00        26.01        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       63.62        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       17.85        10.39         8.02        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       17.03        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       18.28        55.76        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 
        9.53        39.45        43.76        46.65        43.43        42.90 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       42.28        44.91        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 
       29.19        33.53        23.61        22.09        22.06        27.09 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       24.13         8.38        25.08        20.61        21.76        24.69 
TCGA-A6-6653 TCGA-A6-6780 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-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
       56.25         5.03         7.04         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 
       63.98         1.02        38.99         1.02         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
       33.99        21.01        24.00        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 
       61.02        78.08         6.97         2.01        14.01        47.05 
TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       15.95        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
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-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 
       33.01        26.01        20.98        34.03         2.01        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 
       16.08        13.05        34.06        25.02        27.02        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00K TCGA-AA-A00N 
       13.94        38.04        19.00        30.02        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01Z 
        1.02        35.01         1.02        33.04         1.02        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-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       22.03        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
       24.53         5.79        27.42        26.47         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        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4615 
       17.85        19.33        18.84       109.28        58.39        32.94 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       22.36        88.21        49.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 
       11.74        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 
       15.62        51.32        21.99        21.14        82.95         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        25.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.98        30.08        32.02        15.02 
TCGA-CM-5862 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 
        5.03        17.03        15.02        12.00        14.04        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 
       21.99        14.99        12.99        14.04        11.01        12.95 
TCGA-CM-6675 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.01        10.06        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       19.59        56.09        55.92        20.19        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 
       16.14        15.58        12.39        12.43        14.30         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.35        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-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-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 
       31.96        11.11        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
        1.55        34.42        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6299 
        0.53        47.41        35.31       133.18         8.35        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 
       67.30        53.62        44.68        85.48        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.43        13.78        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        11.90        70.03 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 
       39.48        17.23        43.04        37.97        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       16.83        24.36        20.02        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3592 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-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        20.98         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       32.98         0.99         0.99        19.04        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       36.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       32.02        36.03        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       20.98         6.02        37.02         9.07         1.02         1.02 
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         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        47.44        78.12         7.17        21.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       26.04        31.00        12.00        10.98        44.02        25.97 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       12.62       126.44        41.36        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
        3.48         4.18        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.34         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         9.96        49.51        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                        129.27                         148.01 
  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE 
                         24.03                          21.37 
[1] "0.2 - 129.3 (24.0)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.3"
D47V2, continuous
D47V3, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    78  34
  DEL PEAK 23(10P15.3) WILD-TYPE 370 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     78   34
  DEL PEAK 23(10P15.3) WILD-TYPE  370  128
        clus
vv       DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  COLON                            78                            370
  RECTUM                           34                            128
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 23(10P15.3) MUTATED        19        0        7        21         1
  DEL PEAK 23(10P15.3) WILD-TYPE      85        1       30       151        11
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 23(10P15.3) MUTATED           1         1          6         16
  DEL PEAK 23(10P15.3) WILD-TYPE         1        23          9         68
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 23(10P15.3) MUTATED           13       17         6         1
  DEL PEAK 23(10P15.3) WILD-TYPE         42       46        18         1
D47V4, multiclass
            clus
vv           DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  STAGE I                              19                             85
  STAGE IA                              0                              1
  STAGE II                              7                             30
  STAGE IIA                            21                            151
  STAGE IIB                             1                             11
  STAGE IIC                             1                              1
  STAGE III                             1                             23
  STAGE IIIA                            6                              9
  STAGE IIIB                           16                             68
  STAGE IIIC                           13                             42
  STAGE IV                             17                             46
  STAGE IVA                             6                             18
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 23(10P15.3) MUTATED     2  23  74  14
  DEL PEAK 23(10P15.3) WILD-TYPE  18  82 343  55
D47V5, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  T1                            2                             18
  T2                           23                             82
  T3                           74                            343
  T4                           14                             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
  DEL PEAK 23(10P15.3) MUTATED    52  32  29
  DEL PEAK 23(10P15.3) WILD-TYPE 294 118  86
D47V6, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  N0                           52                            294
  N1                           32                            118
  N2                           29                             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"
D47V7, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    78  24
  DEL PEAK 23(10P15.3) WILD-TYPE 375  64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     78   24
  DEL PEAK 23(10P15.3) WILD-TYPE  375   64
   clus
vv  DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  0                           78                            375
  1                           24                             64
[1] 2 2
[1] FALSE
D47V8, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    52  61
  DEL PEAK 23(10P15.3) WILD-TYPE 237 264
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     52   61
  DEL PEAK 23(10P15.3) WILD-TYPE  237  264
        clus
vv       DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  FEMALE                           52                            237
  MALE                             61                            264
[1] 2 2
[1] FALSE
D47V9, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED    92   9
  DEL PEAK 23(10P15.3) WILD-TYPE 390  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED     92    9
  DEL PEAK 23(10P15.3) WILD-TYPE  390   20
     clus
vv    DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  NO                            92                            390
  YES                            9                             20
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 23(10P15.3) MUTATED                     70
  DEL PEAK 23(10P15.3) WILD-TYPE                  312
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(10P15.3) MUTATED                               8
  DEL PEAK 23(10P15.3) WILD-TYPE                            54
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 23(10P15.3) MUTATED                      30
  DEL PEAK 23(10P15.3) WILD-TYPE                   116
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 23(10P15.3) MUTATED                                4
  DEL PEAK 23(10P15.3) WILD-TYPE                              9
D47V10, multiclass
                                clus
vv                               DEL PEAK 23(10P15.3) MUTATED
  COLON ADENOCARCINOMA                                     70
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    30
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               DEL PEAK 23(10P15.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      312
  COLON MUCINOUS ADENOCARCINOMA                              54
  RECTAL ADENOCARCINOMA                                     116
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 23(10P15.3) MUTATED    84   0   6   6
  DEL PEAK 23(10P15.3) WILD-TYPE 362   6  31  23
D47V11, multiclass
    clus
vv   DEL PEAK 23(10P15.3) MUTATED DEL PEAK 23(10P15.3) WILD-TYPE
  R0                           84                            362
  R1                            0                              6
  R2                            6                             31
  RX                            6                             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"
D47V12, continuous
D47V13, binary
                                cls
clus                               0   1
  DEL PEAK 23(10P15.3) MUTATED     1  69
  DEL PEAK 23(10P15.3) WILD-TYPE   4 283
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(10P15.3) MUTATED      1   69
  DEL PEAK 23(10P15.3) WILD-TYPE    4  283
                        clus
vv                       DEL PEAK 23(10P15.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       DEL PEAK 23(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            283
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 24(10Q21.1) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 24(10Q21.1) MUTATED   106  27
  DEL PEAK 24(10Q21.1) WILD-TYPE 360 101
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                           133                            461 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                            27                            101 
$`DEL PEAK 24(10Q21.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 
       24.33        45.60        13.02        19.99         6.05        36.00 
TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-G4-6314 TCGA-G4-6625 
       85.05        24.03         2.01        50.99        35.93        91.79 
TCGA-NH-A8F7 TCGA-AG-A00H TCGA-G5-6641 TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 
       17.85        25.97        26.43         1.61        39.45        43.76 
TCGA-A6-2680 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 
       35.11        34.65        32.45        30.44        32.71        29.16 
TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B 
       22.52        25.18        20.61        23.87        61.84        56.25 
TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3548 TCGA-AA-3549 
        9.63         1.02         6.97        38.99        33.99        21.01 
TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3848 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3968 
       50.04        37.05        10.06        31.07        17.03        21.99 
TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01Q TCGA-AA-A01X 
        7.96        34.03        42.02        10.98         1.02        26.01 
TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-A5EK 
       39.98         5.03        41.00        24.53        22.42        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-A8YK TCGA-AZ-4614 TCGA-AZ-4684 
       14.50        16.31         0.20        18.84         5.65        65.00 
TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5797 TCGA-CA-6716 
       62.79        29.56         3.19        12.69        12.59        12.20 
TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 
       14.30         8.02        29.06        22.03         5.03        15.02 
TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 
       15.02        29.03        13.02        15.02        11.08        11.08 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6926 
       17.75        43.27        15.12        17.85         7.53         9.04 
TCGA-D5-6929 TCGA-D5-6931 TCGA-D5-6932 TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6461 
       13.41        12.00        11.38        35.97       117.07        11.11 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A6GC TCGA-RU-A8FL 
       55.04        61.91        26.04        46.75        12.79        38.70 
TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6672 
       60.13        46.92        13.55        34.49        16.83        24.59 
TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3591 
       65.98        32.02        36.03        20.05        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3887 
       34.03        34.03         6.05        29.98         1.02        36.95 
TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A026 
        1.02        19.99        13.94         6.02        23.01         1.94 
TCGA-AG-A02X TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 
       41.00        44.78        48.20        13.97        51.98        25.05 
TCGA-DC-6683 TCGA-DY-A1DE TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 
       25.05       129.27        17.00        16.31        16.41        28.57 
TCGA-F5-6864 
       12.46 

$`DEL PEAK 24(10Q21.1) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 
        0.99        17.95        23.01        19.99         0.92        19.00 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 
       19.04        19.04        14.93        31.07        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       24.00        26.01        24.00        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 
      106.75       100.01         1.94        49.08         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 
       23.51        63.62        22.09        35.80        26.17        79.69 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 
       55.76        15.62         4.80        12.66         9.53        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 
       43.76        43.43        42.90        42.28        44.91        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 
       37.05        37.25        37.02        32.75        36.53        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6652 
       27.09        24.13         8.38        25.08        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-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        5.03         7.04         3.02        37.05        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02         1.02         9.07        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3555 
       29.00        26.01        12.99        14.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 
        2.01        14.01        47.05        47.01        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
        5.98         5.03        26.99        10.06        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-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
       37.02         0.00        17.03         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       36.03        32.05         0.99        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       27.02        27.02        13.94        38.04        19.00        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-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        32.02        12.00 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01T 
       31.00        31.00        38.07        35.01         1.02        33.04 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02O 
        1.02        37.02        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-6889 
       22.03        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
        5.79        27.42        26.47         0.46         0.92        27.09 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95        33.01        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 
       19.33       109.28        58.39         1.41        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 
       22.36        88.21        49.41         6.77        12.10         5.23 
TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
       11.74        12.36        12.46        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       51.32        21.99        21.14        82.95         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        25.02        26.04        27.02 
TCGA-CM-4752 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 
       13.02        22.98        30.08        32.02        15.02        17.03 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 
       15.02        12.00        14.04        16.04        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6678 
       12.99        14.04        11.01        12.95        13.05        11.01 
TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       10.06        12.03        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6537 
       55.92        20.19        20.42        18.25        25.48         4.80 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 
       17.13        12.49        16.14        15.58        12.39        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-7000 
       12.43        14.30         9.44        11.64        13.35        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-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-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 
      119.93        60.79        98.24        95.18         8.61        31.96 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 
       65.85        53.62        44.68        85.48        39.42        36.00 
TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       26.43        13.78        74.79        18.18        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
       19.33         9.93        15.65        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        11.90        70.03 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 
       39.48        17.23        43.04        37.97        37.74        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.36        20.02        86.63        11.84        36.03        12.00 
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-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       17.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       46.03        20.98        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97        38.96        61.97        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       13.78        47.44        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       26.04        31.00        12.00        31.00        10.98        44.02 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.97        12.62       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         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 
       20.91        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-F5-6812 
        9.96        49.51        42.35         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        47.08 

  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                        129.27                         148.01 
  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE 
                         23.87                          21.76 
[1] "0.2 - 129.3 (23.9)" "0.0 - 148.0 (21.8)"
[1] "hr=" "1.1"
D48V2, continuous
D48V3, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED    97  40
  DEL PEAK 24(10Q21.1) WILD-TYPE 351 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED     97   40
  DEL PEAK 24(10Q21.1) WILD-TYPE  351  122
        clus
vv       DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  COLON                            97                            351
  RECTUM                           40                            122
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 24(10Q21.1) MUTATED        20        0        8        32         2
  DEL PEAK 24(10Q21.1) WILD-TYPE      84        1       29       140        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(10Q21.1) MUTATED           1         1          5         20
  DEL PEAK 24(10Q21.1) WILD-TYPE         1        23         10         64
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 24(10Q21.1) MUTATED           18       20         6         1
  DEL PEAK 24(10Q21.1) WILD-TYPE         37       43        18         1
D48V4, multiclass
            clus
vv           DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  STAGE I                              20                             84
  STAGE IA                              0                              1
  STAGE II                              8                             29
  STAGE IIA                            32                            140
  STAGE IIB                             2                             10
  STAGE IIC                             1                              1
  STAGE III                             1                             23
  STAGE IIIA                            5                             10
  STAGE IIIB                           20                             64
  STAGE IIIC                           18                             37
  STAGE IV                             20                             43
  STAGE IVA                             6                             18
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 24(10Q21.1) MUTATED     3  24  96  15
  DEL PEAK 24(10Q21.1) WILD-TYPE  17  81 321  54
D48V5, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  T1                            3                             17
  T2                           24                             81
  T3                           96                            321
  T4                           15                             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 24(10Q21.1) MUTATED    69  36  33
  DEL PEAK 24(10Q21.1) WILD-TYPE 277 114  82
D48V6, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  N0                           69                            277
  N1                           36                            114
  N2                           33                             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"
D48V7, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED    99  26
  DEL PEAK 24(10Q21.1) WILD-TYPE 354  62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED     99   26
  DEL PEAK 24(10Q21.1) WILD-TYPE  354   62
   clus
vv  DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  0                           99                            354
  1                           26                             62
[1] 2 2
[1] FALSE
D48V8, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED    63  75
  DEL PEAK 24(10Q21.1) WILD-TYPE 226 250
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED     63   75
  DEL PEAK 24(10Q21.1) WILD-TYPE  226  250
        clus
vv       DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  FEMALE                           63                            226
  MALE                             75                            250
[1] 2 2
[1] FALSE
D48V9, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED   106  15
  DEL PEAK 24(10Q21.1) WILD-TYPE 376  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED    106   15
  DEL PEAK 24(10Q21.1) WILD-TYPE  376   14
     clus
vv    DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  NO                           106                            376
  YES                           15                             14
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 24(10Q21.1) MUTATED                     90
  DEL PEAK 24(10Q21.1) WILD-TYPE                  292
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(10Q21.1) MUTATED                               7
  DEL PEAK 24(10Q21.1) WILD-TYPE                            55
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 24(10Q21.1) MUTATED                      34
  DEL PEAK 24(10Q21.1) WILD-TYPE                   112
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 24(10Q21.1) MUTATED                                6
  DEL PEAK 24(10Q21.1) WILD-TYPE                              7
D48V10, multiclass
                                clus
vv                               DEL PEAK 24(10Q21.1) MUTATED
  COLON ADENOCARCINOMA                                     90
  COLON MUCINOUS ADENOCARCINOMA                             7
  RECTAL ADENOCARCINOMA                                    34
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 24(10Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      292
  COLON MUCINOUS ADENOCARCINOMA                              55
  RECTAL ADENOCARCINOMA                                     112
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 24(10Q21.1) MUTATED    98   2  12   7
  DEL PEAK 24(10Q21.1) WILD-TYPE 348   4  25  22
D48V11, multiclass
    clus
vv   DEL PEAK 24(10Q21.1) MUTATED DEL PEAK 24(10Q21.1) WILD-TYPE
  R0                           98                            348
  R1                            2                              4
  R2                           12                             25
  RX                            7                             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"
D48V12, continuous
D48V13, binary
                                cls
clus                               0   1
  DEL PEAK 24(10Q21.1) MUTATED     4  79
  DEL PEAK 24(10Q21.1) WILD-TYPE   1 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(10Q21.1) MUTATED      4   79
  DEL PEAK 24(10Q21.1) WILD-TYPE    1  273
                        clus
vv                       DEL PEAK 24(10Q21.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       DEL PEAK 24(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            273
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 25(10Q23.31) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(10Q23.31) MUTATED   129  26
  DEL PEAK 25(10Q23.31) WILD-TYPE 337 102
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                            155                             439 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                             26                             102 
$`DEL PEAK 25(10Q23.31) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3552 TCGA-AA-3556 
       24.33        45.60        13.94        24.16        13.02        23.01 
TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 
       19.99         6.05        36.00        85.05        31.07        24.03 
TCGA-AA-3952 TCGA-AA-3972 TCGA-DM-A285 TCGA-NH-A8F7 TCGA-AG-A00H TCGA-BM-6198 
        2.01        50.99         5.88        17.85        25.97        21.24 
TCGA-G5-6641 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-4107 
       26.43        39.45        43.76        42.28        35.11        32.45 
TCGA-A6-5659 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6648 TCGA-A6-6654 
       30.44        32.71        29.16        22.52        25.18        23.87 
TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3526 
       61.84         9.63         1.02         6.97         9.07        19.07 
TCGA-AA-3548 TCGA-AA-3664 TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3841 
       33.99        54.02        50.04        11.01        37.05        36.95 
TCGA-AA-3851 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q 
       33.07        31.07        17.03         7.96        34.03        42.02 
TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6901 
       10.98        33.04        26.01        39.98        41.00        22.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A54L TCGA-AY-A69D 
       16.44         0.46        14.50        16.31        17.26        17.85 
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        12.69 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6719 TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5344 
       12.59        12.20        14.30         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        43.27        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-F4-6461 TCGA-F4-6807 TCGA-F4-6808 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       11.11        43.04        33.67        55.04        61.91        36.00 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-NH-A6GC TCGA-QG-A5YW TCGA-RU-A8FL 
       26.04        13.78        46.75        12.79        29.46        38.70 
TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 
       60.13        46.92        39.48        13.55        34.49        24.59 
TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       65.98        32.02         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 
       34.03        50.04         6.05        29.98        37.02        19.04 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-4021 TCGA-AG-A008 
       36.95         1.02        25.02        19.99         3.98        13.94 
TCGA-AG-A011 TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6897 TCGA-CI-6622 TCGA-CI-6624 
       37.02         1.02        41.00        26.43        44.78        48.20 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF 
       13.97        51.98        25.05        25.05       129.27        24.13 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
        3.48         4.18        17.00        16.34        16.31        16.41 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 
       11.97        28.57        36.49        12.46        47.08 

$`DEL PEAK 25(10Q23.31) WILD-TYPE`
TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 
       14.53         1.02        58.03        13.02        24.03        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 
       36.03         8.05        19.07        34.03         0.99        17.95 
TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.99         0.92        19.00        19.04        19.04        14.93 
TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       29.98        12.99        24.00        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 
       10.88        75.95       106.75       100.01         1.94        49.08 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 
       26.17        91.79        79.69        10.39         8.02        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       19.99        17.03        17.03        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       51.98        18.28        55.76        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        1.61         9.53        46.65        43.76        43.43        42.90 
TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 
       44.91        16.57        37.05        37.25        37.02        34.65 
TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 
       32.75        36.53        32.91        31.63        29.19        33.53 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       23.61        22.09        22.06        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 
       25.08        20.61        21.76        24.69        24.39        20.12 
TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3488 
       19.66        20.28        16.24        24.92        56.25         5.03 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        7.04         3.02        37.05        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 
       38.99         1.02         0.00        29.00        29.00        26.01 
TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       12.99        14.01        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08         6.97         2.01        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.05        47.01        15.02         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 
       10.06        35.05         0.99        25.02         1.02        17.98 
TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 
        0.00         0.00        36.03        32.05         0.99        53.00 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       27.02        18.05        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02        27.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        32.02        12.00        31.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 
        1.02        35.01         1.02         1.02        37.02        51.98 
TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
        2.96         2.01         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 
       18.05        40.96        12.16        83.24        24.53         5.79 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 
       27.42        26.47         0.92        27.09         0.95        33.01 
TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
        0.20        21.44        17.82        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41        32.94         5.13        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5255 
       49.41         6.77        12.10         5.23        11.74        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 
       12.46        12.39        12.59        12.76        10.06        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         2.01       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5348 
       37.02        25.02        26.04        27.02        13.02        22.98 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       32.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 
       16.04        21.99        14.99        12.99        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 
       12.95        11.01        12.03        45.40        54.61        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 
       55.92        20.19        20.42        25.48        15.12         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       17.13        16.14        15.58        12.39        12.43        14.30 
TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-6932 TCGA-D5-7000 
        9.44        11.64        13.35        12.00        11.38        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
      119.70        24.43        38.20        92.75        49.91        12.59 
TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
        7.50        44.32       131.51       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G 
       14.04        26.47        81.37       119.93        35.97        60.79 
TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6463 
      117.07        98.24        95.18         8.61        31.96        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 
       82.39        74.56        67.30        65.85        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       85.48        39.42        26.43        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 
       32.98         8.42        31.30        21.90        11.90        70.03 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       17.23        43.04        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.36        20.02        86.63        11.84        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3599 
        7.07        36.03        20.05        24.00         2.01        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        17.95 
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-4022 TCGA-AG-A002 TCGA-AG-A00C 
       36.03        14.04         1.02        46.03        20.98         6.02 
TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       23.01         9.07         1.02        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        38.56         2.50        43.20        27.55 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6623 TCGA-CL-5917 
       19.46         6.05        33.17        13.78        47.44        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       31.00        10.98        44.02        25.97        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       41.36        57.24        51.48        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
       20.91        18.28        15.85        17.69         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       42.35         0.39        32.19        19.66        37.18        38.14 
TCGA-F5-6863 
       11.87 

  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                           0.46                            0.00 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                         140.38                          148.01 
  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE 
                          24.16                           21.37 
[1] "0.5 - 140.4 (24.2)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.3"
D49V2, continuous
D49V3, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED   108  51
  DEL PEAK 25(10Q23.31) WILD-TYPE 340 111
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED    108   51
  DEL PEAK 25(10Q23.31) WILD-TYPE  340  111
        clus
vv       DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  COLON                            108                             340
  RECTUM                            51                             111
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 25(10Q23.31) MUTATED        21        1        7        41         3
  DEL PEAK 25(10Q23.31) WILD-TYPE      83        0       30       131         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(10Q23.31) MUTATED           1         5          7         22
  DEL PEAK 25(10Q23.31) WILD-TYPE         1        19          8         62
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 25(10Q23.31) MUTATED           17       22         6         2
  DEL PEAK 25(10Q23.31) WILD-TYPE         38       41        18         0
D49V4, multiclass
            clus
vv           DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  STAGE I                               21                              83
  STAGE IA                               1                               0
  STAGE II                               7                              30
  STAGE IIA                             41                             131
  STAGE IIB                              3                               9
  STAGE IIC                              1                               1
  STAGE III                              5                              19
  STAGE IIIA                             7                               8
  STAGE IIIB                            22                              62
  STAGE IIIC                            17                              38
  STAGE IV                              22                              41
  STAGE IVA                              6                              18
  STAGE IVB                              2                               0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 25(10Q23.31) MUTATED     3  24 114  17
  DEL PEAK 25(10Q23.31) WILD-TYPE  17  81 303  52
D49V5, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  T1                             3                              17
  T2                            24                              81
  T3                           114                             303
  T4                            17                              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 25(10Q23.31) MUTATED    78  44  37
  DEL PEAK 25(10Q23.31) WILD-TYPE 268 106  78
D49V6, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  N0                            78                             268
  N1                            44                             106
  N2                            37                              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"
D49V7, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED   116  29
  DEL PEAK 25(10Q23.31) WILD-TYPE 337  59
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED    116   29
  DEL PEAK 25(10Q23.31) WILD-TYPE  337   59
   clus
vv  DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  0                           116                             337
  1                            29                              59
[1] 2 2
[1] FALSE
D49V8, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED    76  84
  DEL PEAK 25(10Q23.31) WILD-TYPE 213 241
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED     76   84
  DEL PEAK 25(10Q23.31) WILD-TYPE  213  241
        clus
vv       DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  FEMALE                            76                             213
  MALE                              84                             241
[1] 2 2
[1] FALSE
D49V9, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED   129  13
  DEL PEAK 25(10Q23.31) WILD-TYPE 353  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED    129   13
  DEL PEAK 25(10Q23.31) WILD-TYPE  353   16
     clus
vv    DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  NO                            129                             353
  YES                            13                              16
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 25(10Q23.31) MUTATED                     97
  DEL PEAK 25(10Q23.31) WILD-TYPE                  285
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(10Q23.31) MUTATED                               9
  DEL PEAK 25(10Q23.31) WILD-TYPE                            53
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 25(10Q23.31) MUTATED                      42
  DEL PEAK 25(10Q23.31) WILD-TYPE                   104
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 25(10Q23.31) MUTATED                                7
  DEL PEAK 25(10Q23.31) WILD-TYPE                              6
D49V10, multiclass
                                clus
vv                               DEL PEAK 25(10Q23.31) MUTATED
  COLON ADENOCARCINOMA                                      97
  COLON MUCINOUS ADENOCARCINOMA                              9
  RECTAL ADENOCARCINOMA                                     42
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               DEL PEAK 25(10Q23.31) WILD-TYPE
  COLON ADENOCARCINOMA                                       285
  COLON MUCINOUS ADENOCARCINOMA                               53
  RECTAL ADENOCARCINOMA                                      104
  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"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 25(10Q23.31) MUTATED   118   1  12   6
  DEL PEAK 25(10Q23.31) WILD-TYPE 328   5  25  23
D49V11, multiclass
    clus
vv   DEL PEAK 25(10Q23.31) MUTATED DEL PEAK 25(10Q23.31) WILD-TYPE
  R0                           118                             328
  R1                             1                               5
  R2                            12                              25
  RX                             6                              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"
D49V12, continuous
D49V13, binary
                                 cls
clus                                0   1
  DEL PEAK 25(10Q23.31) MUTATED     3  97
  DEL PEAK 25(10Q23.31) WILD-TYPE   2 255
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(10Q23.31) MUTATED      3   97
  DEL PEAK 25(10Q23.31) WILD-TYPE    2  255
                        clus
vv                       DEL PEAK 25(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            97
                        clus
vv                       DEL PEAK 25(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             255
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 26(10Q25.2) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(10Q25.2) MUTATED   117  33
  DEL PEAK 26(10Q25.2) WILD-TYPE 349  95
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                           150                            444 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                            33                             95 
$`DEL PEAK 26(10Q25.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3562 TCGA-AA-3662 
       24.33        45.60        37.05        13.02        19.99         6.05 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-A024 
       36.00        85.05        24.03         2.01        50.99        39.06 
TCGA-DM-A285 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AG-3890 TCGA-AG-A00H TCGA-BM-6198 
        5.88        91.79        17.85        17.03        25.97        21.24 
TCGA-G5-6641 TCGA-3L-AA1B TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 
       26.43        15.62        39.45        43.76        42.28        35.11 
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        56.25         9.63         5.03 
TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3548 TCGA-AA-3666 
        1.02         6.97         9.07        29.00        33.99         2.01 
TCGA-AA-3673 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3811 TCGA-AA-3818 
       50.04        11.01        37.05         5.03        10.06         0.99 
TCGA-AA-3841 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3866 TCGA-AA-3989 TCGA-AA-A00F 
       36.95        33.07         0.99        17.03         7.96        34.03 
TCGA-AA-A00Q TCGA-AA-A01D TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02O TCGA-AA-A02W 
       42.02        10.98        33.04        26.01         0.92        41.00 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-A69D 
       22.42        26.47        16.44        14.50        16.31        17.85 
TCGA-AZ-4614 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5797 
        5.65        65.00        62.79        29.56         3.19        12.59 
TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-5341 
       12.20        14.30         2.01        25.02         8.02        29.06 
TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6164 TCGA-CM-6169 
       22.03         5.03        15.02        15.02        29.03        13.02 
TCGA-CM-6170 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6531 TCGA-D5-6534 
       15.02        11.08        11.08        10.06        17.75        43.27 
TCGA-D5-6536 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D7 
       17.85         7.53        10.13         9.04        13.41        13.32 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28F TCGA-F4-6461 TCGA-F4-6807 TCGA-F4-6808 
      140.38       131.51        35.97        11.11        43.04        33.67 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A6GC 
       55.04        61.91        36.00        26.04        46.75        12.79 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 
       38.70        60.13        46.92        39.48        13.55        34.49 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 
       24.59        65.98        32.02        34.03        34.03         6.05 
TCGA-AG-3728 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3909 
       29.98        19.04        36.95         1.02        25.02        19.99 
TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A020 TCGA-AG-A02X 
       36.03         3.98        13.94        37.02         1.02        41.00 
TCGA-AH-6897 TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6682 
       26.43        48.20        13.97        51.98        44.02        25.05 
TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6514 
       25.05       129.27        24.13         4.18        17.00        16.31 
TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 
       16.41        11.97        28.57        36.49        12.46        47.08 

$`DEL PEAK 26(10Q25.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3713 
       17.95        23.01        19.99         0.92        19.00        19.04 
TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 
       19.04        14.93        31.07        29.98        12.99        24.00 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AD-6548 
       26.01        24.00        19.07        38.04        21.99        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94        49.08        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 
       22.09        35.80        26.17        79.69        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       13.94        19.99        17.03        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       51.98        18.28        55.76         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 
        9.53        46.65        43.76        43.43        42.90        44.91 
TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 
       16.57        37.05        37.25        37.02        34.65        32.75 
TCGA-A6-3810 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 
       36.53        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-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 
       21.76        24.69        24.39        20.12        19.66        20.28 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 
       16.24        24.92         7.04         3.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
       63.98         1.02        38.99         1.02        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3549 TCGA-AA-3553 
       29.00        26.01        12.99        14.01        21.01        24.00 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       29.95        20.98        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3681 
       54.02        14.01        47.05        47.01        15.02         5.98 
TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       26.99        35.05        25.02         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 
        0.00        36.03        32.05        31.07        53.00        27.02 
TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 
       18.05        31.00         2.01        24.00        33.01        26.01 
TCGA-AA-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-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       34.06        25.02        27.02        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       19.00        30.02        18.05        18.05         4.01        27.02 
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-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q 
       32.02        12.00        31.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02E 
       35.01         1.02         1.02        37.02        51.98         2.96 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         5.03        22.03        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 
       40.96        12.16        83.24        24.53         5.79        27.42 
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        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       21.44        17.82        17.26        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-5407 
       58.39         1.41        32.94         5.13        22.36        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5254 
       49.41         6.77        12.10         5.23        11.74        12.69 
TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.46        12.39        12.59        12.76        10.06 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.99        21.14        82.95       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 
       32.02        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        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 
       19.59        56.09        55.92        20.19        20.42        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       25.48        15.12         4.80        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 
       13.35        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        31.96        35.74        35.74         6.18        47.87 
TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        34.42        41.42        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 
       65.85        53.62        44.68        85.48        39.42        26.43 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        74.79        18.18        10.98        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        16.80        42.77        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2690 
        8.42        31.30        21.90        11.90        70.03        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       43.04        37.97        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       20.02        86.63        11.84        36.03        12.00         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
       36.03        20.05        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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99         1.02        17.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       14.01        48.03        32.02        28.04        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98         6.02        23.01         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        38.96        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        2.50        43.20        27.55        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        47.44        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       25.05        26.04        31.00        12.00        31.00        10.98 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
       25.97        12.62       126.44        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         3.48        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.34         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        49.51        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19        19.66        37.18        38.14        11.87 

  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                          0.92                           0.00 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE 
                        24.460                         21.405 
[1] "0.9 - 140.4 (24.5)" "0.0 - 148.0 (21.4)"
[1] "hr=" "1.1"
D50V2, continuous
D50V3, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED   108  47
  DEL PEAK 26(10Q25.2) WILD-TYPE 340 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED    108   47
  DEL PEAK 26(10Q25.2) WILD-TYPE  340  115
        clus
vv       DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  COLON                           108                            340
  RECTUM                           47                            115
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 26(10Q25.2) MUTATED        19        0        9        42         1
  DEL PEAK 26(10Q25.2) WILD-TYPE      85        1       28       130        11
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 26(10Q25.2) MUTATED           1         6          6         21
  DEL PEAK 26(10Q25.2) WILD-TYPE         1        18          9         63
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 26(10Q25.2) MUTATED           19       22         6         1
  DEL PEAK 26(10Q25.2) WILD-TYPE         36       41        18         1
D50V4, multiclass
            clus
vv           DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  STAGE I                              19                             85
  STAGE IA                              0                              1
  STAGE II                              9                             28
  STAGE IIA                            42                            130
  STAGE IIB                             1                             11
  STAGE IIC                             1                              1
  STAGE III                             6                             18
  STAGE IIIA                            6                              9
  STAGE IIIB                           21                             63
  STAGE IIIC                           19                             36
  STAGE IV                             22                             41
  STAGE IVA                             6                             18
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 26(10Q25.2) MUTATED     3  22 115  15
  DEL PEAK 26(10Q25.2) WILD-TYPE  17  83 302  54
D50V5, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  T1                            3                             17
  T2                           22                             83
  T3                          115                            302
  T4                           15                             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 26(10Q25.2) MUTATED    75  42  38
  DEL PEAK 26(10Q25.2) WILD-TYPE 271 108  77
D50V6, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  N0                           75                            271
  N1                           42                            108
  N2                           38                             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"
D50V7, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED   115  28
  DEL PEAK 26(10Q25.2) WILD-TYPE 338  60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED    115   28
  DEL PEAK 26(10Q25.2) WILD-TYPE  338   60
   clus
vv  DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  0                          115                            338
  1                           28                             60
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED    74  82
  DEL PEAK 26(10Q25.2) WILD-TYPE 215 243
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED     74   82
  DEL PEAK 26(10Q25.2) WILD-TYPE  215  243
        clus
vv       DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  FEMALE                           74                            215
  MALE                             82                            243
[1] 2 2
[1] FALSE
D50V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED   121  11
  DEL PEAK 26(10Q25.2) WILD-TYPE 361  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED    121   11
  DEL PEAK 26(10Q25.2) WILD-TYPE  361   18
     clus
vv    DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  NO                           121                            361
  YES                           11                             18
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 26(10Q25.2) MUTATED                     98
  DEL PEAK 26(10Q25.2) WILD-TYPE                  284
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(10Q25.2) MUTATED                               9
  DEL PEAK 26(10Q25.2) WILD-TYPE                            53
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 26(10Q25.2) MUTATED                      39
  DEL PEAK 26(10Q25.2) WILD-TYPE                   107
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 26(10Q25.2) MUTATED                                7
  DEL PEAK 26(10Q25.2) WILD-TYPE                              6
D50V10, multiclass
                                clus
vv                               DEL PEAK 26(10Q25.2) MUTATED
  COLON ADENOCARCINOMA                                     98
  COLON MUCINOUS ADENOCARCINOMA                             9
  RECTAL ADENOCARCINOMA                                    39
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK 26(10Q25.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      284
  COLON MUCINOUS ADENOCARCINOMA                              53
  RECTAL ADENOCARCINOMA                                     107
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(10Q25.2) MUTATED   114   2  12   6
  DEL PEAK 26(10Q25.2) WILD-TYPE 332   4  25  23
D50V11, multiclass
    clus
vv   DEL PEAK 26(10Q25.2) MUTATED DEL PEAK 26(10Q25.2) WILD-TYPE
  R0                          114                            332
  R1                            2                              4
  R2                           12                             25
  RX                            6                             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"
D50V12, continuous
D50V13, binary
                                cls
clus                               0   1
  DEL PEAK 26(10Q25.2) MUTATED     2  92
  DEL PEAK 26(10Q25.2) WILD-TYPE   3 260
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(10Q25.2) MUTATED      2   92
  DEL PEAK 26(10Q25.2) WILD-TYPE    3  260
                        clus
vv                       DEL PEAK 26(10Q25.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           92
                        clus
vv                       DEL PEAK 26(10Q25.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            260
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 27(11Q22.3) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(11Q22.3) MUTATED    82  22
  DEL PEAK 27(11Q22.3) WILD-TYPE 384 106
  DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE 
                           104                            490 
  DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE 
                            22                            106 
$`DEL PEAK 27(11Q22.3) MUTATED`
TCGA-A6-2681 TCGA-A6-6649 TCGA-AA-3522 TCGA-AA-3662 TCGA-AA-3692 TCGA-AA-3860 
       45.60        24.16        37.05         6.05        36.00        31.07 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AG-3611 TCGA-BM-6198 TCGA-A6-2671 
       12.99         2.01        50.99        13.94        21.24        43.76 
TCGA-A6-2683 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-6138 TCGA-A6-6651 
       16.57        36.53        32.45        30.44        22.52        21.76 
TCGA-A6-6654 TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3558 TCGA-AA-3666 
       23.87         5.03         6.97         9.07        20.98         2.01 
TCGA-AA-3680 TCGA-AA-3855 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3956 TCGA-AA-3966 
       11.01        32.05        18.05        24.00        34.03         2.01 
TCGA-AA-3968 TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E 
       21.99        34.03        42.02        32.02        33.04         2.96 
TCGA-AA-A02F TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AU-3779 
       39.98        40.96         5.79        22.42        16.44        14.50 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4323 TCGA-CA-5256 
        0.95         0.20        17.85        19.33         1.41        12.46 
TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       12.20         2.01        30.08         5.03        15.02        15.02 
TCGA-CM-6163 TCGA-CM-6172 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6536 
       14.04        11.01        11.01        45.40        20.19        17.85 
TCGA-D5-6924 TCGA-DM-A1D0 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-F4-6461 TCGA-G4-6315 
       14.30       130.65        49.91         7.50        11.11        61.91 
TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GC TCGA-RU-A8FL TCGA-AF-2691 
       36.00        46.75        18.18        12.79        38.70        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 
       13.55        37.97        29.98        24.36        24.59        32.02 
TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 
        7.07        46.03        34.03        34.03         2.01         6.05 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-A008 
        0.99        32.98        19.04        17.95         1.02        13.94 
TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-6155 
        1.02        41.00        38.56        43.20        27.55        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6508 TCGA-EI-6509 
       10.98        44.02        12.62        24.13        20.91        17.00 
TCGA-EI-6881 TCGA-EI-7004 
       16.41         8.45 

$`DEL PEAK 27(11Q22.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       24.33        13.94        14.53         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3672 
       13.02        17.95        23.01        19.99        19.99         0.92 
TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3867 
       19.00        85.05        19.04        19.04        14.93        24.03 
TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L 
       29.98        24.00        26.01        24.00        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       75.95       106.75       100.01         1.94        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
       19.99        17.03        17.03        25.97        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       31.00        51.98        18.28        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 
        4.80        12.66         1.61         9.53        39.45        46.65 
TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       43.76        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-5656 
       37.05        37.25        37.02        34.65        32.75        32.91 
TCGA-A6-5657 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       31.63        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 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-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
       25.18        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        56.25         9.63 
TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 
        7.04         3.02         1.02        37.05        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         1.02        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        26.01        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        29.95        13.94        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 
       54.02        14.01        50.04        47.05        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       36.95        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       17.03        27.02        31.00         2.01        33.01        26.01 
TCGA-AA-3955 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       20.98        16.08        13.05        34.06        25.02        27.02 
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-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U 
       18.05        18.05         4.01        27.02         0.99        17.03 
TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
       14.99        34.98        15.02        15.02        10.98        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-A029 TCGA-AA-A02H TCGA-AA-A02J 
        1.02        26.01        37.02        51.98         2.01         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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       83.24        24.53        27.42        26.47         0.46         0.92 
TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        16.31        33.01        21.44        17.82        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
       18.84       109.28        58.39         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 
       12.36        12.39        12.59        12.59        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       14.30        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14        82.95       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        25.02        26.04         8.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       13.02        29.06        22.03        22.98        32.02        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-6674 
       14.99        12.99        13.02        15.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 
       13.05        11.08        11.08        10.06        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        55.92        20.42        17.75        18.25 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       25.48        43.27        15.12         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 
       16.14        15.58         7.53        12.39        10.13        12.43 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 
       11.38        10.26       119.70        24.43        38.20        92.75 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       13.32        12.59       140.38        44.32       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-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 
       31.96        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       34.42        41.42        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 
       47.41        35.31       133.18         8.35        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U 
       39.42        26.43        26.04        13.78        74.79        10.98 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        21.90        60.13 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 
       11.90        70.03        46.92        39.48        17.23        34.49 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       37.74        16.83        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       36.03        12.00        36.03        20.05        24.00         1.02 
TCGA-AG-3592 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       34.03        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       20.98         7.99        29.98        37.02         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-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         9.07         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       38.96        61.97        38.04         2.50        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       12.00        31.00        51.98        25.97        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 
        3.48         4.18        20.55        19.96        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE 
                        130.65                         148.01 
  DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE 
                         19.76                          22.67 
[1] "0.2 - 130.7 (19.8)" "0.0 - 148.0 (22.7)"
[1] "hr=" "1.3"
D51V2, continuous
D51V3, binary
                                cls
clus                               0   1
  DEL PEAK 27(11Q22.3) MUTATED    70  36
  DEL PEAK 27(11Q22.3) WILD-TYPE 378 126
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q22.3) MUTATED     70   36
  DEL PEAK 27(11Q22.3) WILD-TYPE  378  126
        clus
vv       DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE
  COLON                            70                            378
  RECTUM                           36                            126
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 27(11Q22.3) MUTATED        22        0        4        26         0
  DEL PEAK 27(11Q22.3) WILD-TYPE      82        1       33       146        12
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 27(11Q22.3) MUTATED           0         6          2         15
  DEL PEAK 27(11Q22.3) WILD-TYPE         2        18         13         69
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 27(11Q22.3) MUTATED           11       14         4         1
  DEL PEAK 27(11Q22.3) WILD-TYPE         44       49        20         1
D51V4, multiclass
            clus
vv           DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE
  STAGE I                              22                             82
  STAGE IA                              0                              1
  STAGE II                              4                             33
  STAGE IIA                            26                            146
  STAGE IIB                             0                             12
  STAGE IIC                             0                              2
  STAGE III                             6                             18
  STAGE IIIA                            2                             13
  STAGE IIIB                           15                             69
  STAGE IIIC                           11                             44
  STAGE IV                             14                             49
  STAGE IVA                             4                             20
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 27(11Q22.3) MUTATED     4  19  72  15
  DEL PEAK 27(11Q22.3) WILD-TYPE  16  86 345  54
D51V5, multiclass
    clus
vv   DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE
  T1                            4                             16
  T2                           19                             86
  T3                           72                            345
  T4                           15                             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 27(11Q22.3) MUTATED    53  32  24
  DEL PEAK 27(11Q22.3) WILD-TYPE 293 118  91
D51V6, multiclass
    clus
vv   DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE
  N0                           53                            293
  N1                           32                            118
  N2                           24                             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"
D51V7, binary
                                cls
clus                               0   1
  DEL PEAK 27(11Q22.3) MUTATED    76  18
  DEL PEAK 27(11Q22.3) WILD-TYPE 377  70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q22.3) MUTATED     76   18
  DEL PEAK 27(11Q22.3) WILD-TYPE  377   70
   clus
vv  DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE
  0                           76                            377
  1                           18                             70
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 27(11Q22.3) MUTATED    54  56
  DEL PEAK 27(11Q22.3) WILD-TYPE 235 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q22.3) MUTATED     54   56
  DEL PEAK 27(11Q22.3) WILD-TYPE  235  269
        clus
vv       DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE
  FEMALE                           54                            235
  MALE                             56                            269
[1] 2 2
[1] FALSE
D51V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(11Q22.3) MUTATED    82   9
  DEL PEAK 27(11Q22.3) WILD-TYPE 400  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q22.3) MUTATED     82    9
  DEL PEAK 27(11Q22.3) WILD-TYPE  400   20
     clus
vv    DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE
  NO                            82                            400
  YES                            9                             20
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 27(11Q22.3) MUTATED                     62
  DEL PEAK 27(11Q22.3) WILD-TYPE                  320
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(11Q22.3) MUTATED                               8
  DEL PEAK 27(11Q22.3) WILD-TYPE                            54
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 27(11Q22.3) MUTATED                      29
  DEL PEAK 27(11Q22.3) WILD-TYPE                   117
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 27(11Q22.3) MUTATED                                6
  DEL PEAK 27(11Q22.3) WILD-TYPE                              7
D51V10, multiclass
                                clus
vv                               DEL PEAK 27(11Q22.3) MUTATED
  COLON ADENOCARCINOMA                                     62
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    29
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 27(11Q22.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      320
  COLON MUCINOUS ADENOCARCINOMA                              54
  RECTAL ADENOCARCINOMA                                     117
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(11Q22.3) MUTATED    78   0   9   4
  DEL PEAK 27(11Q22.3) WILD-TYPE 368   6  28  25
D51V11, multiclass
    clus
vv   DEL PEAK 27(11Q22.3) MUTATED DEL PEAK 27(11Q22.3) WILD-TYPE
  R0                           78                            368
  R1                            0                              6
  R2                            9                             28
  RX                            4                             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"
D51V12, continuous
D51V13, binary
                                cls
clus                               0   1
  DEL PEAK 27(11Q22.3) MUTATED     1  56
  DEL PEAK 27(11Q22.3) WILD-TYPE   4 296
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(11Q22.3) MUTATED      1   56
  DEL PEAK 27(11Q22.3) WILD-TYPE    4  296
                        clus
vv                       DEL PEAK 27(11Q22.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           56
                        clus
vv                       DEL PEAK 27(11Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            296
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 28(12P13.1) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(12P13.1) MUTATED    64  25
  DEL PEAK 28(12P13.1) WILD-TYPE 402 103
  DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE 
                            89                            505 
  DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE 
                            25                            103 
$`DEL PEAK 28(12P13.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3552 TCGA-AA-3688 TCGA-AA-3867 TCGA-AA-3952 
       24.33        45.60        13.02        19.00        24.03         2.01 
TCGA-AA-3972 TCGA-CK-5912 TCGA-G4-6586 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-G5-6641 
       50.99        49.08        35.80        17.85        10.39        26.43 
TCGA-4N-A93T TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-6652 
        4.80        43.76        34.65        36.53        30.44        24.69 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 
       20.28        61.84         9.63        26.01        14.01        33.99 
TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-A01F 
       78.08         2.01        50.04        31.07        17.03        32.02 
TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK TCGA-AZ-4684 
       33.04         2.96         5.79        22.42        16.44        65.00 
TCGA-CA-5256 TCGA-CA-6715 TCGA-CM-4750 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6164 
       12.46        12.59         8.02         5.03        14.04        29.03 
TCGA-CM-6170 TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6679 TCGA-D5-6533 TCGA-D5-6535 
       15.02        11.01        11.08        10.06        25.48        15.12 
TCGA-D5-6898 TCGA-D5-6932 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-F4-6460 TCGA-F4-6461 
        7.53        11.38        13.32        12.59        31.96        11.11 
TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 TCGA-NH-A50U TCGA-QL-A97D 
       43.04        65.85        61.91        36.00        10.98        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
       38.70        60.13        43.04        13.55        37.97        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3728 
       24.36        20.02        36.03        34.03        34.03        29.98 
TCGA-AG-3731 TCGA-AG-3898 TCGA-AG-4021 TCGA-AG-A00C TCGA-AG-A026 TCGA-AH-6544 
       37.02        48.03         3.98         6.02         1.94        38.56 
TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6508 
       33.17        13.97        10.98        24.13        51.48        20.91 
TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       17.00        16.31        16.41        28.57        36.49 

$`DEL PEAK 28(12P13.1) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
        0.99        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.92        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3979 
       31.07        29.98        12.99        24.00        26.01        24.00 
TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       19.07        38.04        21.99        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 
        5.88        28.21        23.51        63.62        35.93        22.09 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       26.17        91.79        79.69         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       17.03        17.03        25.97        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4T-AA8H 
       51.98        21.24        18.28        55.76        15.62        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        1.61         9.53        39.45        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       42.90        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.25        37.02        32.75        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       29.19        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 
       29.16        27.09        22.52        24.13         8.38        25.08 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 
       25.18        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        56.25         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       29.00        29.00        12.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       20.98        13.94        61.02         6.97        54.02        14.01 
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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       36.03        32.05         0.99        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       34.03         2.01        21.99        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         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-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
       27.02        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K 
       15.02        15.02        10.98        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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O 
       37.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 
       83.24        24.53        27.42        26.47         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        33.01         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
       21.44        17.82        17.26        17.85        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       22.36        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.20        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         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        25.02        26.04        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        32.02        15.02 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 
       15.02        15.02        17.03        15.02        12.00        16.04 
TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6674 
       21.99        14.99        12.99        13.02        14.04        12.95 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5537 TCGA-D5-5538 
       13.05        11.08        11.01        12.03        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 
       19.59        56.09        55.92        20.19        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       18.25        43.27        17.85         4.80        17.13        12.49 
TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       16.14        15.58        12.39        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A1HB 
       49.91       140.38         7.50        44.32       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-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6459 
       35.97        60.79       117.07        98.24        95.18         8.61 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       41.42        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
      133.18         8.35        82.39        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 
       44.68        55.04        85.48        39.42        26.43        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV 
       13.78        46.75        74.79        18.18        19.33        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YW 
        9.93        15.65        12.79        16.80        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 
       32.98         8.42        31.30        11.90        70.03        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6672 
       39.48        17.23        34.49        37.74        16.83        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        65.98        11.84        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
       36.03        20.05        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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 
       19.99        20.98         7.99         0.99        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       19.99        28.04        36.03        14.04         1.02        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        13.94        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1.02        49.97        38.96        61.97        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       21.01        25.05        26.04        31.00        12.00        31.00 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       51.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24       129.27        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        4.18        20.55        19.96        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34         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-F5-6810 
       11.97         8.45         9.96        49.51        42.35         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       32.19        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE 
                          1.94                           0.00 
  DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE 
                         78.08                         148.01 
  DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE 
                         24.13                          21.99 
[1] "1.9 - 78.1 (24.1)"  "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D52V2, continuous
D52V3, binary
                                cls
clus                               0   1
  DEL PEAK 28(12P13.1) MUTATED    60  29
  DEL PEAK 28(12P13.1) WILD-TYPE 388 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(12P13.1) MUTATED     60   29
  DEL PEAK 28(12P13.1) WILD-TYPE  388  133
        clus
vv       DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE
  COLON                            60                            388
  RECTUM                           29                            133
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 28(12P13.1) MUTATED        14        0        5        17         2
  DEL PEAK 28(12P13.1) WILD-TYPE      90        1       32       155        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(12P13.1) MUTATED           0         2          5         12
  DEL PEAK 28(12P13.1) WILD-TYPE         2        22         10         72
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 28(12P13.1) MUTATED           12       11         8         0
  DEL PEAK 28(12P13.1) WILD-TYPE         43       52        16         2
D52V4, multiclass
            clus
vv           DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE
  STAGE I                              14                             90
  STAGE IA                              0                              1
  STAGE II                              5                             32
  STAGE IIA                            17                            155
  STAGE IIB                             2                             10
  STAGE IIC                             0                              2
  STAGE III                             2                             22
  STAGE IIIA                            5                             10
  STAGE IIIB                           12                             72
  STAGE IIIC                           12                             43
  STAGE IV                             11                             52
  STAGE IVA                             8                             16
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 28(12P13.1) MUTATED     4  14  65   9
  DEL PEAK 28(12P13.1) WILD-TYPE  16  91 352  60
D52V5, multiclass
    clus
vv   DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE
  T1                            4                             16
  T2                           14                             91
  T3                           65                            352
  T4                            9                             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 28(12P13.1) MUTATED    42  32  18
  DEL PEAK 28(12P13.1) WILD-TYPE 304 118  97
D52V6, multiclass
    clus
vv   DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE
  N0                           42                            304
  N1                           32                            118
  N2                           18                             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"
D52V7, binary
                                cls
clus                               0   1
  DEL PEAK 28(12P13.1) MUTATED    58  19
  DEL PEAK 28(12P13.1) WILD-TYPE 395  69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(12P13.1) MUTATED     58   19
  DEL PEAK 28(12P13.1) WILD-TYPE  395   69
   clus
vv  DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE
  0                           58                            395
  1                           19                             69
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(12P13.1) MUTATED    45  47
  DEL PEAK 28(12P13.1) WILD-TYPE 244 278
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(12P13.1) MUTATED     45   47
  DEL PEAK 28(12P13.1) WILD-TYPE  244  278
        clus
vv       DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE
  FEMALE                           45                            244
  MALE                             47                            278
[1] 2 2
[1] FALSE
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 28(12P13.1) MUTATED    76   5
  DEL PEAK 28(12P13.1) WILD-TYPE 406  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(12P13.1) MUTATED     76    5
  DEL PEAK 28(12P13.1) WILD-TYPE  406   24
     clus
vv    DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE
  NO                            76                            406
  YES                            5                             24
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 28(12P13.1) MUTATED                     57
  DEL PEAK 28(12P13.1) WILD-TYPE                  325
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(12P13.1) MUTATED                               2
  DEL PEAK 28(12P13.1) WILD-TYPE                            60
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 28(12P13.1) MUTATED                      28
  DEL PEAK 28(12P13.1) WILD-TYPE                   118
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 28(12P13.1) MUTATED                                1
  DEL PEAK 28(12P13.1) WILD-TYPE                             12
D52V10, multiclass
                                clus
vv                               DEL PEAK 28(12P13.1) MUTATED
  COLON ADENOCARCINOMA                                     57
  COLON MUCINOUS ADENOCARCINOMA                             2
  RECTAL ADENOCARCINOMA                                    28
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 28(12P13.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      325
  COLON MUCINOUS ADENOCARCINOMA                              60
  RECTAL ADENOCARCINOMA                                     118
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 28(12P13.1) MUTATED    66   1   6   4
  DEL PEAK 28(12P13.1) WILD-TYPE 380   5  31  25
D52V11, multiclass
    clus
vv   DEL PEAK 28(12P13.1) MUTATED DEL PEAK 28(12P13.1) WILD-TYPE
  R0                           66                            380
  R1                            1                              5
  R2                            6                             31
  RX                            4                             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"
D52V12, continuous
D52V13, binary
                                cls
clus                               0   1
  DEL PEAK 28(12P13.1) MUTATED     0  58
  DEL PEAK 28(12P13.1) WILD-TYPE   5 294
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(12P13.1) MUTATED      0   58
  DEL PEAK 28(12P13.1) WILD-TYPE    5  294
                        clus
vv                       DEL PEAK 28(12P13.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           58
                        clus
vv                       DEL PEAK 28(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            294
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 29(12Q21.33) MUTATION ANALYSIS
D53V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 29(12Q21.33) MUTATED    64  24
  DEL PEAK 29(12Q21.33) WILD-TYPE 402 104
  DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE 
                             88                             506 
  DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE 
                             24                             104 
$`DEL PEAK 29(12Q21.33) MUTATED`
TCGA-A6-2677 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3867 TCGA-AA-3952 
       24.33        13.02        17.95        23.01        24.03         2.01 
TCGA-AA-3972 TCGA-AA-3979 TCGA-CK-5912 TCGA-AG-A014 TCGA-G5-6233 TCGA-5M-AAT4 
       50.99        24.00        49.08        15.95        18.28         1.61 
TCGA-A6-2671 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-5659 TCGA-A6-5662 TCGA-A6-6782 
       43.76        34.65        36.53        30.44        23.61        20.28 
TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
       61.84        56.25         9.63        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3968 
       33.99        50.04        37.05        31.07        17.03        21.99 
TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-A5EK 
       32.02        33.04         2.96         5.79        22.42        16.44 
TCGA-AU-3779 TCGA-AY-6196 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CM-4750 
       14.50         0.20         3.19        12.46        12.20         8.02 
TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6172 
       29.06         5.03        14.04        29.03        15.02        11.01 
TCGA-CM-6675 TCGA-CM-6677 TCGA-D5-6533 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D8 
       13.05        11.08        25.48        13.41        11.38        12.59 
TCGA-DM-A1DA TCGA-F4-6460 TCGA-F4-6807 TCGA-G4-6303 TCGA-G4-6315 TCGA-G4-6317 
        7.50        31.96        43.04        65.85        61.91        36.00 
TCGA-NH-A8F8 TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-AF-2691 TCGA-AF-3400 
       16.80         8.42        38.70        60.13        43.04        34.49 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3574 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3728 
       29.98        24.36        36.03        34.03        34.03        29.98 
TCGA-AG-3732 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-A00Y TCGA-AG-A032 TCGA-AH-6544 
       32.98        48.03        36.03        23.01        38.04        38.56 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6514 
       13.97        10.98       129.27        24.13        17.00        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6812 
       16.41        11.51        28.57        36.49 

$`DEL PEAK 29(12Q21.33) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       45.60        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       34.03         0.99        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3986 
       31.07        29.98        12.99        24.00        26.01        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 
       10.88        75.95       106.75       100.01         1.94         5.88 
TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
       28.21        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       26.17        91.79        79.69        17.85        10.39         8.02 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A015 
       13.94        19.99        17.03        17.03        25.97        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       31.00        51.98        21.24        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 
        4.80        12.66         9.53        39.45        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-4107 TCGA-A6-5656 
       37.05        37.25        37.02        32.75        32.45        32.91 
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-A6-6138 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-A6-6650 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-AA-3488 TCGA-AA-3489 
       20.12        19.66        16.24        24.92         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 
        1.02        38.99         1.02         9.07        19.07         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       29.00        29.00        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 
       13.94        61.02        78.08         6.97        54.02         2.01 
TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 
       14.01        47.05        47.01        15.02        11.01         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 
        0.00        17.03        10.06         0.00        33.07         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 
       36.03        32.05         0.99        53.00        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 
       31.00         2.01        24.00        33.01        26.01        20.98 
TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       34.03         2.01        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D 
       27.02         7.96        27.02        13.94        38.04        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O 
       30.02        34.03        18.05        18.05         4.01        27.02 
TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       42.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P 
       15.02        10.98        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         1.02        26.01        37.02 
TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       51.98        39.98         2.01         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 
       41.00        39.98        18.05        40.96        12.16        83.24 
TCGA-AD-6890 TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       24.53        27.42        26.47         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        33.01        21.44        17.82        17.26 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.85        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        5.65        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.76        10.06        14.30        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 
       70.16        15.62        51.32        21.99        21.14        82.95 
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        25.02 
TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 
       26.04        27.02        13.02        22.03        22.98        30.08 
TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 
       32.02        15.02        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-6169 
       12.00        16.04        21.99        14.99        12.99        13.02 
TCGA-CM-6171 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       14.04        12.95        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 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        43.27        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD 
       11.64        13.35        12.00        10.26       119.70        24.43 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 
       38.20       130.65        92.75        49.91        13.32       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-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-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       98.24        95.18         8.61        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6808 
        6.18        47.87         1.55        34.42        41.42        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 
       13.25         0.53        47.41        35.31       133.18         8.35 
TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       82.39        74.56        67.30        53.62        44.68        55.04 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       85.48        39.42        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA 
       74.79        18.18        10.98        19.33        19.33         9.93 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z2 
       15.65        12.79        42.77        29.46        32.98        31.30 
TCGA-QL-A97D TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.90        11.90        70.03        46.92        39.48        17.23 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       13.55        37.97        37.74        16.83        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        65.98        11.84        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
       36.03        20.05        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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       19.99        20.98         7.99         0.99        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       19.99        28.04        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        13.94         6.02        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        49.97         1.94        38.96        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       33.17        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       31.00        51.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
       12.62       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
        3.48         4.18        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       15.85        17.69        16.34         8.61        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        49.51        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE 
                         129.27                          148.01 
  DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE 
                         24.015                          21.600 
[1] "0.2 - 129.3 (24.0)" "0.0 - 148.0 (21.6)"
[1] "hr=" "1.4"
D53V2, continuous
D53V3, binary
                                 cls
clus                                0   1
  DEL PEAK 29(12Q21.33) MUTATED    62  27
  DEL PEAK 29(12Q21.33) WILD-TYPE 386 135
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(12Q21.33) MUTATED     62   27
  DEL PEAK 29(12Q21.33) WILD-TYPE  386  135
        clus
vv       DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE
  COLON                             62                             386
  RECTUM                            27                             135
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 29(12Q21.33) MUTATED        15        0        3        19         2
  DEL PEAK 29(12Q21.33) WILD-TYPE      89        1       34       153        10
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 29(12Q21.33) MUTATED           1         1          4         10
  DEL PEAK 29(12Q21.33) WILD-TYPE         1        23         11         74
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 29(12Q21.33) MUTATED           14       11         4         1
  DEL PEAK 29(12Q21.33) WILD-TYPE         41       52        20         1
D53V4, multiclass
            clus
vv           DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE
  STAGE I                               15                              89
  STAGE IA                               0                               1
  STAGE II                               3                              34
  STAGE IIA                             19                             153
  STAGE IIB                              2                              10
  STAGE IIC                              1                               1
  STAGE III                              1                              23
  STAGE IIIA                             4                              11
  STAGE IIIB                            10                              74
  STAGE IIIC                            14                              41
  STAGE IV                              11                              52
  STAGE IVA                              4                              20
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 29(12Q21.33) MUTATED     3  15  65   7
  DEL PEAK 29(12Q21.33) WILD-TYPE  17  90 352  62
D53V5, multiclass
    clus
vv   DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE
  T1                             3                              17
  T2                            15                              90
  T3                            65                             352
  T4                             7                              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 29(12Q21.33) MUTATED    43  24  23
  DEL PEAK 29(12Q21.33) WILD-TYPE 303 126  92
D53V6, multiclass
    clus
vv   DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE
  N0                            43                             303
  N1                            24                             126
  N2                            23                              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"
D53V7, binary
                                 cls
clus                                0   1
  DEL PEAK 29(12Q21.33) MUTATED    62  16
  DEL PEAK 29(12Q21.33) WILD-TYPE 391  72
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(12Q21.33) MUTATED     62   16
  DEL PEAK 29(12Q21.33) WILD-TYPE  391   72
   clus
vv  DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE
  0                            62                             391
  1                            16                              72
[1] 2 2
[1] FALSE
D53V8, binary
                                 cls
clus                                0   1
  DEL PEAK 29(12Q21.33) MUTATED    40  50
  DEL PEAK 29(12Q21.33) WILD-TYPE 249 275
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(12Q21.33) MUTATED     40   50
  DEL PEAK 29(12Q21.33) WILD-TYPE  249  275
        clus
vv       DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE
  FEMALE                            40                             249
  MALE                              50                             275
[1] 2 2
[1] FALSE
D53V9, binary
                                 cls
clus                                0   1
  DEL PEAK 29(12Q21.33) MUTATED    75   5
  DEL PEAK 29(12Q21.33) WILD-TYPE 407  24
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(12Q21.33) MUTATED     75    5
  DEL PEAK 29(12Q21.33) WILD-TYPE  407   24
     clus
vv    DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE
  NO                             75                             407
  YES                             5                              24
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 29(12Q21.33) MUTATED                     59
  DEL PEAK 29(12Q21.33) WILD-TYPE                  323
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(12Q21.33) MUTATED                               2
  DEL PEAK 29(12Q21.33) WILD-TYPE                            60
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 29(12Q21.33) MUTATED                      26
  DEL PEAK 29(12Q21.33) WILD-TYPE                   120
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 29(12Q21.33) MUTATED                                1
  DEL PEAK 29(12Q21.33) WILD-TYPE                             12
D53V10, multiclass
                                clus
vv                               DEL PEAK 29(12Q21.33) MUTATED
  COLON ADENOCARCINOMA                                      59
  COLON MUCINOUS ADENOCARCINOMA                              2
  RECTAL ADENOCARCINOMA                                     26
  RECTAL MUCINOUS ADENOCARCINOMA                             1
                                clus
vv                               DEL PEAK 29(12Q21.33) WILD-TYPE
  COLON ADENOCARCINOMA                                       323
  COLON MUCINOUS ADENOCARCINOMA                               60
  RECTAL ADENOCARCINOMA                                      120
  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"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 29(12Q21.33) MUTATED    72   0   3   3
  DEL PEAK 29(12Q21.33) WILD-TYPE 374   6  34  26
D53V11, multiclass
    clus
vv   DEL PEAK 29(12Q21.33) MUTATED DEL PEAK 29(12Q21.33) WILD-TYPE
  R0                            72                             374
  R1                             0                               6
  R2                             3                              34
  RX                             3                              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"
D53V12, continuous
D53V13, binary
                                 cls
clus                                0   1
  DEL PEAK 29(12Q21.33) MUTATED     1  53
  DEL PEAK 29(12Q21.33) WILD-TYPE   4 299
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(12Q21.33) MUTATED      1   53
  DEL PEAK 29(12Q21.33) WILD-TYPE    4  299
                        clus
vv                       DEL PEAK 29(12Q21.33) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            53
                        clus
vv                       DEL PEAK 29(12Q21.33) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             299
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 30(14Q11.2) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(14Q11.2) MUTATED   163  41
  DEL PEAK 30(14Q11.2) WILD-TYPE 303  87
  DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE 
                           204                            390 
  DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE 
                            41                             87 
$`DEL PEAK 30(14Q11.2) MUTATED`
TCGA-A6-4105 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 
       14.53        24.03        36.03        19.07        34.03        13.02 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3867 
       23.01        19.99        19.99        19.00        85.05        24.03 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AZ-6608 
       12.99        50.99        26.01        38.04        21.99         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AG-3890 
       49.08         5.88        28.21        91.79        17.85        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       17.03        25.97        21.24        18.28        55.76        26.43 
TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 
        4.80        39.45        43.76        42.28        35.11        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5662 
       34.65        36.53        32.45        32.91        30.44        23.61 
TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 
       22.52        24.13        25.08        20.61        21.76        24.69 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3511 
       23.87        20.28        61.84         5.03         7.04         6.97 
TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       38.99         9.07        13.94         2.01        14.01        50.04 
TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 
       47.01        37.05        10.06        25.02        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       17.03        17.03        18.05        34.03        21.99        16.08 
TCGA-AA-3975 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W 
       34.06         7.96        34.03        27.02        42.02        14.99 
TCGA-AA-A017 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-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK 
        2.01        40.96         5.79        22.42        27.42        16.44 
TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
       14.50         0.95        33.01        17.85        18.84       109.28 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5255 
        1.41         5.65        22.36        29.56         5.23        12.36 
TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 
       12.46        12.59        12.20         2.01        25.02         8.02 
TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6172 
       17.03        14.04        29.03        13.02        15.02        11.01 
TCGA-CM-6676 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-6532 
       11.08        10.06        45.40        54.61        56.09        18.25 
TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6924 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XF 
       25.48        15.12        14.30        13.41        11.38        38.20 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A288 TCGA-DM-A28E TCGA-F4-6460 TCGA-F4-6806 
       12.59       140.38        14.04       119.93        31.96        41.42 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6315 
       33.67        13.25         0.53         8.35        82.39        61.91 
TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-RU-A8FL TCGA-SS-A7HO 
       18.18        19.33        15.65        16.80        38.70        60.13 
TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       11.90        39.48        13.55        37.97        34.49        37.74 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3591 
       24.59        65.98        11.84        36.03         7.07        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 
       34.03        34.03        50.04         6.05         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 
       19.99         1.02        17.95        35.01         1.02        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G 
       36.03        14.04         6.02        23.01         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 
       38.04        38.56         6.05        33.17        47.44        48.20 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        25.05        31.00        13.97        51.98        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 
       25.05        25.05       129.27        24.13        51.48        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 
       20.91        17.00        16.34        16.31        16.41        10.78 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 
       11.97        42.35         0.39        32.19        36.49        11.87 

$`DEL PEAK 30(14Q11.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3662 
       13.02        37.05         8.05         0.99        17.95         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
        0.92        36.00        19.04        19.04        14.93        31.07 
TCGA-AA-3870 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A024 
       29.98        24.00         2.01        24.00        19.07        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
      100.01        23.51        63.62        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       26.17        79.69        10.39         8.02        13.94        19.99 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-3L-AA1B TCGA-4T-AA8H 
       15.95        36.03        31.00        51.98        15.62        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 
        1.61         9.53        46.65        43.76        43.43        42.90 
TCGA-A6-2679 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 
       44.91        37.05        37.25        37.02        32.75        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-3492 TCGA-AA-3494 
       16.24        24.92        56.25         9.63         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 
       37.05        35.01        63.98         1.02         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 
       33.99        21.01        24.00        29.95        20.98        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 
       78.08         6.97        54.02        47.05        15.02        11.01 
TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 
        5.98         5.03        26.99        35.05         0.99         1.02 
TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3837 TCGA-AA-3845 TCGA-AA-3848 TCGA-AA-3850 
       17.98        15.95        38.99         0.00        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
       33.07         0.00        36.03        32.05         0.99        31.07 
TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 
       53.00        27.02        31.00         2.01        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 
       26.01        20.98         2.01        13.05        25.02        27.02 
TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        13.94        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01C 
       18.05         4.01         0.99        17.03        34.98        15.02 
TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       10.98        12.00        31.00        38.07         1.02        35.01 
TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J 
        1.02         1.02        37.02        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        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       83.24        24.53        26.47         0.46         0.92        27.09 
TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X 
       16.31         0.20        21.44        17.82        17.26        19.33 
TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       58.39        32.94         5.13        65.00        62.79        88.21 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       49.41         6.77        12.10        11.74         3.19        12.69 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.39        12.59        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       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        32.02        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        55.92        20.19        20.42        17.75        43.27 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        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        13.35        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        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       34.42        43.04        47.41        35.31       133.18        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       39.42        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV 
       74.79        10.98        19.33         9.93        12.79        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 
       29.46        32.98         8.42        31.30        21.90        70.03 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       46.92        17.23        43.04        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 
       20.02        86.63        12.00        32.02        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3605 
       24.00         1.02        46.03         2.01        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 
       15.95        19.99        20.98         7.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       32.98         0.99        19.04        36.95        13.02        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4007 TCGA-AG-4021 
       48.03        25.02        32.02        19.99         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98        13.94        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 
        1.02        49.97        61.97        41.00         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5917 
       27.55        26.43        19.46        13.78        44.78        78.12 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
       21.01        26.04        12.00        31.00        44.02        25.97 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 
       12.62       126.44        41.36        57.24        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 
        4.18        19.96        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        49.51 
TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       28.57        19.66        37.18        38.14        12.46        47.08 

  DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE 
                          0.39                           0.00 
  DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE 
                        22.175                         22.010 
[1] "0.4 - 140.4 (22.2)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D54V2, continuous
D54V3, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q11.2) MUTATED   139  68
  DEL PEAK 30(14Q11.2) WILD-TYPE 309  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q11.2) MUTATED    139   68
  DEL PEAK 30(14Q11.2) WILD-TYPE  309   94
        clus
vv       DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE
  COLON                           139                            309
  RECTUM                           68                             94
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 30(14Q11.2) MUTATED        32        0       12        56         2
  DEL PEAK 30(14Q11.2) WILD-TYPE      72        1       25       116        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 30(14Q11.2) MUTATED           0         8          8         28
  DEL PEAK 30(14Q11.2) WILD-TYPE         2        16          7         56
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 30(14Q11.2) MUTATED           18       25        12         0
  DEL PEAK 30(14Q11.2) WILD-TYPE         37       38        12         2
D54V4, multiclass
            clus
vv           DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE
  STAGE I                              32                             72
  STAGE IA                              0                              1
  STAGE II                             12                             25
  STAGE IIA                            56                            116
  STAGE IIB                             2                             10
  STAGE IIC                             0                              2
  STAGE III                             8                             16
  STAGE IIIA                            8                              7
  STAGE IIIB                           28                             56
  STAGE IIIC                           18                             37
  STAGE IV                             25                             38
  STAGE IVA                            12                             12
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 30(14Q11.2) MUTATED     9  33 148  19
  DEL PEAK 30(14Q11.2) WILD-TYPE  11  72 269  50
D54V5, multiclass
    clus
vv   DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE
  T1                            9                             11
  T2                           33                             72
  T3                          148                            269
  T4                           19                             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 30(14Q11.2) MUTATED   107  64  38
  DEL PEAK 30(14Q11.2) WILD-TYPE 239  86  77
D54V6, multiclass
    clus
vv   DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE
  N0                          107                            239
  N1                           64                             86
  N2                           38                             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"
D54V7, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q11.2) MUTATED   149  37
  DEL PEAK 30(14Q11.2) WILD-TYPE 304  51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q11.2) MUTATED    149   37
  DEL PEAK 30(14Q11.2) WILD-TYPE  304   51
   clus
vv  DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE
  0                          149                            304
  1                           37                             51
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q11.2) MUTATED    98 112
  DEL PEAK 30(14Q11.2) WILD-TYPE 191 213
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q11.2) MUTATED     98  112
  DEL PEAK 30(14Q11.2) WILD-TYPE  191  213
        clus
vv       DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE
  FEMALE                           98                            191
  MALE                            112                            213
[1] 2 2
[1] FALSE
D54V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q11.2) MUTATED   170  13
  DEL PEAK 30(14Q11.2) WILD-TYPE 312  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q11.2) MUTATED    170   13
  DEL PEAK 30(14Q11.2) WILD-TYPE  312   16
     clus
vv    DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE
  NO                           170                            312
  YES                           13                             16
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 30(14Q11.2) MUTATED                    133
  DEL PEAK 30(14Q11.2) WILD-TYPE                  249
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(14Q11.2) MUTATED                               4
  DEL PEAK 30(14Q11.2) WILD-TYPE                            58
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 30(14Q11.2) MUTATED                      66
  DEL PEAK 30(14Q11.2) WILD-TYPE                    80
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 30(14Q11.2) MUTATED                                2
  DEL PEAK 30(14Q11.2) WILD-TYPE                             11
D54V10, multiclass
                                clus
vv                               DEL PEAK 30(14Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    133
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 30(14Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      249
  COLON MUCINOUS ADENOCARCINOMA                              58
  RECTAL ADENOCARCINOMA                                      80
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(14Q11.2) MUTATED   149   2  10  10
  DEL PEAK 30(14Q11.2) WILD-TYPE 297   4  27  19
D54V11, multiclass
    clus
vv   DEL PEAK 30(14Q11.2) MUTATED DEL PEAK 30(14Q11.2) WILD-TYPE
  R0                          149                            297
  R1                            2                              4
  R2                           10                             27
  RX                           10                             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"
D54V12, continuous
D54V13, binary
                                cls
clus                               0   1
  DEL PEAK 30(14Q11.2) MUTATED     2 120
  DEL PEAK 30(14Q11.2) WILD-TYPE   3 232
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(14Q11.2) MUTATED      2  120
  DEL PEAK 30(14Q11.2) WILD-TYPE    3  232
                        clus
vv                       DEL PEAK 30(14Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          120
                        clus
vv                       DEL PEAK 30(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            232
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 31(14Q31.1) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(14Q31.1) MUTATED   168  41
  DEL PEAK 31(14Q31.1) WILD-TYPE 298  87
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                           209                            385 
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                            41                             87 
$`DEL PEAK 31(14Q31.1) MUTATED`
TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3530 TCGA-AA-3531 
       45.60        14.53        24.16        24.03        19.07        34.03 
TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3697 TCGA-AA-3860 
       13.02        23.01        19.99        19.00        85.05        31.07 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 
       24.03        12.99         2.01        50.99        26.01        24.00 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6625 TCGA-NH-A8F7 
       38.04        21.99         1.94        49.08        91.79        17.85 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       17.03        17.03        25.97        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2680 
       26.43         4.80        39.45        43.76        42.28        35.11 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       16.57        34.65        36.53        32.45        32.91        30.44 
TCGA-A6-5662 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 
       23.61        22.52        24.13        25.08        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-3526 TCGA-AA-3542 TCGA-AA-3561 TCGA-AA-3666 
       38.99         9.07        19.07        12.99        13.94         2.01 
TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3685 TCGA-AA-3811 
       14.01        50.04        47.01        15.02        37.05        10.06 
TCGA-AA-3819 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3866 TCGA-AA-3875 
       25.02        36.95        37.02        17.03        17.03        18.05 
TCGA-AA-3930 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3989 TCGA-AA-A00O 
        2.01        21.99        16.08        34.06         7.96        27.02 
TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01T 
       42.02        14.99        15.02        32.02        31.00        33.04 
TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02H TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 
       26.01         2.96         2.01        40.96         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
       27.42        16.44        14.50         0.95        33.01         0.20 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4682 
       17.85        18.84       109.28         1.41         5.65        22.36 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-6715 TCGA-CA-6716 
       29.56         5.23        12.36        12.46        12.59        12.20 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-5868 TCGA-CM-6163 
        2.01        25.02         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 
       45.40        54.61        56.09        18.25        25.48        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        31.96 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6297 
       41.42        33.67        13.25         0.53         8.35        82.39 
TCGA-G4-6315 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-RU-A8FL 
       61.91        18.18        19.33        15.65        16.80        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-A56L 
       60.13        11.90        39.48        13.55        37.74        65.98 
TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       11.84        36.03        46.03        34.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       50.04        12.03         6.05         0.99        37.02         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       19.04         1.02        17.95        35.01         1.02        48.03 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G 
       36.03        14.04         6.02        23.01         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 
       38.04        38.56         6.05        33.17        47.44        48.20 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        7.17        21.01        25.05        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 
       10.98        25.05        25.05       129.27        51.48        20.55 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 
       17.00        16.34        16.31        16.41        10.78        11.97 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 
       42.35         0.39        32.19        36.49        11.87 

$`DEL PEAK 31(14Q31.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3522 
       24.33        13.94         1.02        58.03        13.02        37.05 
TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3662 
       36.03         8.05         0.99        17.95        19.99         6.05 
TCGA-AA-3672 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 
        0.92        36.00        19.04        19.04        14.93        29.98 
TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       24.00        19.07        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6294 
       10.88        75.95       106.75       100.01         5.88        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       23.51        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A014 
       79.69        10.39         8.02        13.94        19.99        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 
       36.03        31.00        51.98        15.62        12.66         1.61 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 
        9.53        46.65        43.76        43.43        42.90        44.91 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5660 
       37.05        37.25        37.02        32.75        31.63        29.19 
TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 
       33.53        22.09        22.06        32.71        29.16        27.09 
TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        25.18        24.39        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       24.92        56.25         9.63         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 
       37.05        35.01        63.98         1.02         1.02         0.00 
TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
       29.00        29.00        26.01        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 
       24.00        29.95        20.98        61.02        78.08         6.97 
TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       54.02        47.05        11.01         5.98         5.03        26.99 
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-3845 TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        10.06         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3877 
       32.05         0.99        31.07        53.00        27.02        31.00 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
       24.00        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       13.05        25.02        27.02        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       19.00        30.02        34.03        18.05        18.05         4.01 
TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01G 
        0.99        17.03        34.98        15.02        10.98        12.00 
TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V 
       31.00        38.07         1.02        35.01         1.02         1.02 
TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R 
       37.02        51.98        39.98         5.03         0.92        22.03 
TCGA-AA-A02W TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 
       41.00        39.98        18.05        12.16        83.24        24.53 
TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6197 
       26.47         0.46         0.92        27.09        16.31        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4616 
       17.82        17.26        19.33        58.39        32.94         5.13 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 
       65.00        62.79        88.21        49.41         6.77        12.10 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6717 
       11.74         3.19        12.69        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4752 TCGA-CM-5341 
       23.05        20.02        37.02        26.04        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        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6165 TCGA-CM-6166 
       15.02        15.02        15.02        12.00        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6677 
       14.99        12.99        14.04        11.01        12.95        11.08 
TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 
       11.01        12.03        19.59        55.92        20.19        20.42 
TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 
       17.75        43.27        17.85         4.80        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        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D8 
      119.70        24.43       130.65        92.75        49.91        12.59 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
       44.32       135.65         7.76       139.17        26.47        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-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6807 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 
       43.04        47.41        35.31       133.18        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50U TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW 
       10.98        19.33         9.93        12.79        42.77        29.46 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 
       32.98         8.42        31.30        21.90        70.03        46.92 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       17.23        43.04        37.97        34.49        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 
       24.36        20.02        24.59        86.63        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 
       32.02         7.07        20.05        24.00         1.02         2.01 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 
        0.99        15.95        19.99        20.98         7.99        29.98 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       32.98         0.99        19.99        36.95        13.02        14.01 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 
       25.02        32.02        19.99        28.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98        13.94        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 
        1.02        49.97        61.97        41.00         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5917 
       27.55        26.43        19.46        13.78        44.78        78.12 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       26.04        12.00        31.00        44.02        25.97        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24        24.13        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        4.18        19.96        20.91        18.28        15.85        17.69 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
        8.61        11.51        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 
       49.51        28.57        19.66        37.18        38.14        12.46 
TCGA-G5-6572 
       47.08 

  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE 
                         21.99                          22.03 
[1] "0.2 - 140.4 (22.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.1"
D55V2, continuous
D55V3, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q31.1) MUTATED   148  68
  DEL PEAK 31(14Q31.1) WILD-TYPE 300  94
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q31.1) MUTATED    148   68
  DEL PEAK 31(14Q31.1) WILD-TYPE  300   94
        clus
vv       DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  COLON                           148                            300
  RECTUM                           68                             94
[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       10        59         2
  DEL PEAK 31(14Q31.1) WILD-TYPE      72        1       27       113        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 31(14Q31.1) MUTATED           0         9          8         31
  DEL PEAK 31(14Q31.1) WILD-TYPE         2        15          7         53
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 31(14Q31.1) MUTATED           19       27        12         1
  DEL PEAK 31(14Q31.1) WILD-TYPE         36       36        12         1
D55V4, multiclass
            clus
vv           DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  STAGE I                              32                             72
  STAGE IA                              0                              1
  STAGE II                             10                             27
  STAGE IIA                            59                            113
  STAGE IIB                             2                             10
  STAGE IIC                             0                              2
  STAGE III                             9                             15
  STAGE IIIA                            8                              7
  STAGE IIIB                           31                             53
  STAGE IIIC                           19                             36
  STAGE IV                             27                             36
  STAGE IVA                            12                             12
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 31(14Q31.1) MUTATED     9  33 156  19
  DEL PEAK 31(14Q31.1) WILD-TYPE  11  72 261  50
D55V5, multiclass
    clus
vv   DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  T1                            9                             11
  T2                           33                             72
  T3                          156                            261
  T4                           19                             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 31(14Q31.1) MUTATED   108  67  42
  DEL PEAK 31(14Q31.1) WILD-TYPE 238  83  73
D55V6, multiclass
    clus
vv   DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  N0                          108                            238
  N1                           67                             83
  N2                           42                             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"
D55V7, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q31.1) MUTATED   155  41
  DEL PEAK 31(14Q31.1) WILD-TYPE 298  47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q31.1) MUTATED    155   41
  DEL PEAK 31(14Q31.1) WILD-TYPE  298   47
   clus
vv  DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  0                          155                            298
  1                           41                             47
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q31.1) MUTATED    95 123
  DEL PEAK 31(14Q31.1) WILD-TYPE 194 202
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q31.1) MUTATED     95  123
  DEL PEAK 31(14Q31.1) WILD-TYPE  194  202
        clus
vv       DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  FEMALE                           95                            194
  MALE                            123                            202
[1] 2 2
[1] FALSE
D55V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q31.1) MUTATED   173  12
  DEL PEAK 31(14Q31.1) WILD-TYPE 309  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q31.1) MUTATED    173   12
  DEL PEAK 31(14Q31.1) WILD-TYPE  309   17
     clus
vv    DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  NO                           173                            309
  YES                           12                             17
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 31(14Q31.1) MUTATED                    141
  DEL PEAK 31(14Q31.1) WILD-TYPE                  241
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(14Q31.1) MUTATED                               4
  DEL PEAK 31(14Q31.1) WILD-TYPE                            58
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 31(14Q31.1) MUTATED                      65
  DEL PEAK 31(14Q31.1) WILD-TYPE                    81
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 31(14Q31.1) MUTATED                                1
  DEL PEAK 31(14Q31.1) WILD-TYPE                             12
D55V10, multiclass
                                clus
vv                               DEL PEAK 31(14Q31.1) MUTATED
  COLON ADENOCARCINOMA                                    141
  COLON MUCINOUS ADENOCARCINOMA                             4
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 31(14Q31.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      241
  COLON MUCINOUS ADENOCARCINOMA                              58
  RECTAL ADENOCARCINOMA                                      81
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 31(14Q31.1) MUTATED   151   2  15  10
  DEL PEAK 31(14Q31.1) WILD-TYPE 295   4  22  19
D55V11, multiclass
    clus
vv   DEL PEAK 31(14Q31.1) MUTATED DEL PEAK 31(14Q31.1) WILD-TYPE
  R0                          151                            295
  R1                            2                              4
  R2                           15                             22
  RX                           10                             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"
D55V12, continuous
D55V13, binary
                                cls
clus                               0   1
  DEL PEAK 31(14Q31.1) MUTATED     2 121
  DEL PEAK 31(14Q31.1) WILD-TYPE   3 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(14Q31.1) MUTATED      2  121
  DEL PEAK 31(14Q31.1) WILD-TYPE    3  231
                        clus
vv                       DEL PEAK 31(14Q31.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          121
                        clus
vv                       DEL PEAK 31(14Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            231
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 32(15Q11.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(15Q11.2) MUTATED   190  50
  DEL PEAK 32(15Q11.2) WILD-TYPE 276  78
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                           240                            354 
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                            50                             78 
$`DEL PEAK 32(15Q11.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       24.33        45.60        37.05        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
       19.99        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 
       12.99        50.99        26.01        24.00       106.75        49.08 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-3612 TCGA-AG-3890 
        5.88        28.21        63.62        91.79        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-G5-6233 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 
       17.03        25.97        18.28        26.43         4.80         1.61 
TCGA-5M-AATE TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 
       39.45        43.76        43.43        42.28        44.91        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       34.65        36.53        32.45        32.91        30.44        29.19 
TCGA-A6-5667 TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6780 
       29.16        22.52        25.08        20.61        21.76        20.12 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       20.28        61.84        56.25         5.03         7.04         1.02 
TCGA-AA-3511 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 
        6.97        29.00        12.99        14.01        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3685 TCGA-AA-3821 
       24.00         2.01        50.04        47.01        37.05         1.02 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3854 
       38.99        36.95        37.02        17.03        10.06        36.03 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3966 TCGA-AA-3968 
        0.99        31.07        17.03        27.02         2.01        21.99 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q 
       13.05        34.06        27.02        19.00        34.03        42.02 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F TCGA-AA-A01K 
       17.03        14.99        15.02        15.02        32.02        31.00 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W TCGA-AD-6899 TCGA-AD-6901 
       33.04        26.01         2.96        41.00         5.79        22.42 
TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 
       27.42        16.44         0.46        14.50        16.31         0.95 
TCGA-AY-5543 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
       33.01        17.85        18.84        65.00        62.79        88.21 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CA-6719 
       29.56         5.23         3.19        12.46        12.20        14.30 
TCGA-CK-4948 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
      148.01         2.01        25.02        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-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       15.02        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6535 
       12.03        54.61        20.19        17.75        25.48        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6932 
       17.13        12.49         7.53        10.13         9.04        11.38 
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-A1HA TCGA-DM-A288 TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 
      131.51        14.04        35.97        95.18        31.96        47.87 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6295 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
        8.35        67.30        65.85        55.04        61.91        36.00 
TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D 
       46.75        10.98        19.33        12.79        29.46        21.90 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 
       38.70        11.90        46.92        43.04        13.55        37.74 
TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 
       29.98        24.59        65.98        11.84        32.02        36.03 
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 
       20.05        46.03        34.03        34.03        34.03         6.05 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3893 
       20.98        29.98         0.99        19.04        19.99        35.01 
TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-A008 
        1.02        25.02        19.99        28.04        14.04        13.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       23.01        37.02         1.02         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 
       38.04        38.56        43.20         6.05        13.78        47.44 
TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
       48.20        31.00        13.97        51.98        25.05        25.05 
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         3.48 
TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        4.18        16.31        16.41        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        42.35        28.57        32.19        36.49        19.66 

$`DEL PEAK 32(15Q11.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       17.95         6.05         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z 
       31.07        24.00         2.01        19.07        38.04        21.99 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 
       39.06        21.37        15.52        25.08        10.88        75.95 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
      100.01         1.94        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 
       26.17        79.69        17.85        10.39         8.02        13.94 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        21.24        55.76 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2676 
       15.62        12.66         9.53        43.76        46.65        42.90 
TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 
       35.11        37.05        37.25        37.02        32.75        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-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       24.13         8.38        25.18        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-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       35.01        63.98         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3558 
       19.07         0.00        29.00        26.01        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 
       47.05        15.02        11.01         5.98         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99        25.02        17.98        15.95 
TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3864 
        0.00         0.00        33.07         0.00        32.05        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-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       20.98        34.03        16.08        25.02         7.96        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-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I 
       27.02         0.99        34.98        10.98        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         1.02        37.02 
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-6889 TCGA-AD-6890 
       39.98        18.05        40.96        12.16        83.24        24.53 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
       26.47         0.92        27.09         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.26        19.33       109.28        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-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       12.76        10.06        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       51.32        21.99        21.14        82.95       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        32.02        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        45.40        19.59        56.09        55.92        20.42 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       18.25        43.27        17.85         4.80        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 
       13.35        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        35.74        35.74         6.18        34.42        41.42 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6304 TCGA-G4-6306 
       35.31       133.18        82.39        74.56        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 
       85.48        39.42        26.43        26.04        13.78        74.79 
TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV 
       18.18        19.33         9.93        15.65        16.80        42.77 
TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2689 
       32.98         8.42        31.30        60.13        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       17.23        37.97        34.49        16.83        24.36        20.02 
TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3584 TCGA-AG-3586 
       86.63        36.03        12.00         7.07        24.00         1.02 
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-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 
        7.99         0.99        37.02        32.98         0.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.95        36.95        13.02        14.01        48.03        32.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       36.03         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 
        9.07         1.02        49.97        61.97         2.50        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
       26.43        19.46        33.17        44.78        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       21.01        25.05        26.04        12.00        31.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6506 
       44.02        25.97        12.62       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-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       16.34         8.61        17.46         8.45         9.96        49.51 
TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
        0.39        37.18        38.14        11.87        12.46        47.08 

  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                          0.46                           0.00 
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                        148.01                         139.17 
  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE 
                        24.015                         21.190 
[1] "0.5 - 148.0 (24.0)" "0.0 - 139.2 (21.2)"
[1] "hr=" "1.1"
D56V2, continuous
D56V3, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q11.2) MUTATED   175  70
  DEL PEAK 32(15Q11.2) WILD-TYPE 273  92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q11.2) MUTATED    175   70
  DEL PEAK 32(15Q11.2) WILD-TYPE  273   92
        clus
vv       DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  COLON                           175                            273
  RECTUM                           70                             92
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 32(15Q11.2) MUTATED        39        0        9        63         3
  DEL PEAK 32(15Q11.2) WILD-TYPE      65        1       28       109         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 32(15Q11.2) MUTATED           1         7          9         34
  DEL PEAK 32(15Q11.2) WILD-TYPE         1        17          6         50
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 32(15Q11.2) MUTATED           28       31        14         2
  DEL PEAK 32(15Q11.2) WILD-TYPE         27       32        10         0
D56V4, multiclass
            clus
vv           DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  STAGE I                              39                             65
  STAGE IA                              0                              1
  STAGE II                              9                             28
  STAGE IIA                            63                            109
  STAGE IIB                             3                              9
  STAGE IIC                             1                              1
  STAGE III                             7                             17
  STAGE IIIA                            9                              6
  STAGE IIIB                           34                             50
  STAGE IIIC                           28                             27
  STAGE IV                             31                             32
  STAGE IVA                            14                             10
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 32(15Q11.2) MUTATED     9  40 173  26
  DEL PEAK 32(15Q11.2) WILD-TYPE  11  65 244  43
D56V5, multiclass
    clus
vv   DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  T1                            9                             11
  T2                           40                             65
  T3                          173                            244
  T4                           26                             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 32(15Q11.2) MUTATED   123  71  54
  DEL PEAK 32(15Q11.2) WILD-TYPE 223  79  61
D56V6, multiclass
    clus
vv   DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  N0                          123                            223
  N1                           71                             79
  N2                           54                             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"
D56V7, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q11.2) MUTATED   175  46
  DEL PEAK 32(15Q11.2) WILD-TYPE 278  42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q11.2) MUTATED    175   46
  DEL PEAK 32(15Q11.2) WILD-TYPE  278   42
   clus
vv  DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  0                          175                            278
  1                           46                             42
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q11.2) MUTATED   110 138
  DEL PEAK 32(15Q11.2) WILD-TYPE 179 187
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q11.2) MUTATED    110  138
  DEL PEAK 32(15Q11.2) WILD-TYPE  179  187
        clus
vv       DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  FEMALE                          110                            179
  MALE                            138                            187
[1] 2 2
[1] FALSE
D56V9, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q11.2) MUTATED   192  14
  DEL PEAK 32(15Q11.2) WILD-TYPE 290  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q11.2) MUTATED    192   14
  DEL PEAK 32(15Q11.2) WILD-TYPE  290   15
     clus
vv    DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  NO                           192                            290
  YES                           14                             15
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 32(15Q11.2) MUTATED                    157
  DEL PEAK 32(15Q11.2) WILD-TYPE                  225
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(15Q11.2) MUTATED                              16
  DEL PEAK 32(15Q11.2) WILD-TYPE                            46
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 32(15Q11.2) MUTATED                      64
  DEL PEAK 32(15Q11.2) WILD-TYPE                    82
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 32(15Q11.2) MUTATED                                5
  DEL PEAK 32(15Q11.2) WILD-TYPE                              8
D56V10, multiclass
                                clus
vv                               DEL PEAK 32(15Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    157
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                    64
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 32(15Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      225
  COLON MUCINOUS ADENOCARCINOMA                              46
  RECTAL ADENOCARCINOMA                                      82
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 32(15Q11.2) MUTATED   176   2  15   8
  DEL PEAK 32(15Q11.2) WILD-TYPE 270   4  22  21
D56V11, multiclass
    clus
vv   DEL PEAK 32(15Q11.2) MUTATED DEL PEAK 32(15Q11.2) WILD-TYPE
  R0                          176                            270
  R1                            2                              4
  R2                           15                             22
  RX                            8                             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"
D56V12, continuous
D56V13, binary
                                cls
clus                               0   1
  DEL PEAK 32(15Q11.2) MUTATED     2 142
  DEL PEAK 32(15Q11.2) WILD-TYPE   3 210
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(15Q11.2) MUTATED      2  142
  DEL PEAK 32(15Q11.2) WILD-TYPE    3  210
                        clus
vv                       DEL PEAK 32(15Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          142
                        clus
vv                       DEL PEAK 32(15Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            210
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 33(15Q15.2) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(15Q15.2) MUTATED   194  49
  DEL PEAK 33(15Q15.2) WILD-TYPE 272  79
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                           243                            351 
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                            49                             79 
$`DEL PEAK 33(15Q15.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       24.33        45.60        37.05        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
       19.99        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 
       12.99        50.99        24.00       106.75        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 
       28.21        63.62        91.79        13.94        19.99        17.03 
TCGA-AG-4008 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-3L-AA1B 
       17.03        25.97        21.24        18.28        26.43        15.62 
TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
        4.80         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 
       42.28        44.91        16.57        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        56.25 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3542 
        5.03         7.04         1.02         6.97         9.07        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3673 
       14.01        33.99        21.01        24.00         2.01        50.04 
TCGA-AA-3678 TCGA-AA-3680 TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
       47.01        11.01        37.05        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 
       17.03        10.06        33.07        36.03         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 
       17.03         2.01        21.99        13.05        34.06        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-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W 
       15.02        31.00        33.04        26.01         2.96        41.00 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 
        5.79        22.42        27.42        16.44        14.50        16.31 
TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK 
        0.95        33.01         0.20        17.85        19.33        18.84 
TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       65.00        62.79        88.21        29.56         5.23         3.19 
TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 
       12.46        12.20       148.01         2.01        25.02        27.02 
TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 
       13.02        29.06         5.03        15.02        17.03        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 
       29.03        16.04        15.02        13.05        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6533 
       11.01        10.06        12.03        54.61        20.19        25.48 
TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 
       15.12         7.53        10.13         9.04        13.41        11.38 
TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA 
      130.65        92.75        13.32        12.59       140.38       131.51 
TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 
       35.97        95.18        31.96        47.87         1.55        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 
       33.67        13.25         0.53        47.41         8.35        65.85 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A50U 
       55.04        61.91        36.00        26.04        46.75        10.98 
TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H 
       19.33        12.79        29.46        21.90        38.70        11.90 
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 
       46.92        43.04        13.55        37.74        29.98        24.59 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       65.98        11.84        32.02        36.03        20.05        24.00 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3725 
       46.03        34.03        34.03        34.03         6.05        20.98 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 
        0.99        29.98        32.98         0.99        19.04        19.99 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       35.01         1.02        25.02        19.99        28.04        14.04 
TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G 
       13.94        23.01        37.02         1.02         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6621 
       41.00        38.04        38.56        43.20         6.05        13.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
       47.44        48.20         7.17        31.00        13.97        51.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       25.05        25.05        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 
        3.48         4.18        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        42.35        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       32.19        36.49        19.66 

$`DEL PEAK 33(15Q15.2) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       17.95         6.05         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       31.07        24.00         2.01        26.01        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 
       75.95       100.01         1.94        23.51        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 
       35.80        26.17        79.69        17.85        10.39         8.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 TCGA-4T-AA8H 
       15.95        36.03        31.00        51.98        55.76        12.66 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 
        9.53        46.65        42.90        35.11        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 
       37.02        32.75        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-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 
       24.69        24.39        23.87        19.66        16.24        24.92 
TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        9.63         3.02        37.05        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
       38.99         1.02        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       26.01        29.95        20.98        13.94        61.02        78.08 
TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3681 
        6.97        54.02        14.01        47.05        15.02         5.98 
TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
        1.02        17.98        15.95         0.00         0.00         0.00 
TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 
       32.05        53.00        27.02        18.05        31.00         2.01 
TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 
       24.00        33.01        26.01        20.98        34.03        16.08 
TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E 
       25.02         7.96        27.02        13.94        38.04        30.02 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       18.05        18.05         4.01        27.02         0.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
       35.01         1.02         1.02        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5820 
       40.96        12.16        83.24        24.53        26.47         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        17.26       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 
       58.39         1.41         5.65        32.94         5.13        22.36 
TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 
       49.41         6.77        12.10        11.74        12.69        12.36 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.39        12.59        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
       17.56        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       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        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6166 TCGA-CM-6167 
       15.02        15.02        15.02        12.00        21.99        14.99 
TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-D5-5537 
       12.99        13.02        14.04        11.01        12.95        45.40 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 
       19.59        56.09        55.92        20.42        17.75        18.25 
TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 
       43.27        17.85         4.80        17.13        12.49        16.14 
TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6927 TCGA-D5-6928 
       15.58        12.39        12.43        14.30         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF 
       13.35        12.00        10.26       119.70        24.43        38.20 
TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
       49.91         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28G TCGA-DM-A28H 
       14.04        26.47        81.37       119.93        60.79       117.07 
TCGA-DM-A28K TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 
       98.24         8.61        11.11        35.74        35.74         6.18 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 
       34.42        41.42        35.31       133.18        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 
       67.30        53.62        44.68        85.48        39.42        26.43 
TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB 
       13.78        74.79        18.18        19.33         9.93        15.65 
TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO 
       16.80        42.77        32.98         8.42        31.30        60.13 
TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 
       70.03        39.48        17.23        37.97        34.49        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       24.36        20.02        86.63        36.03        12.00         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-3885 
       19.99         7.99        37.02         0.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 
       36.95        13.02        14.01        48.03        32.02        36.03 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A016 
        1.02         3.98        46.03        20.98         6.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
        1.02        49.97        61.97         2.50        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
       19.46        33.17        44.78        78.12        21.01        25.05 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       26.04        12.00        31.00        10.98        44.02        25.97 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       12.62       126.44       129.27        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6917 
       20.91        17.00        18.28        17.69        16.34        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 
        8.45         9.96        49.51         0.39        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                        148.01                         139.17 
  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE 
                         23.01                          21.44 
[1] "0.2 - 148.0 (23.0)" "0.0 - 139.2 (21.4)"
[1] "hr=" "1.1"
D57V2, continuous
D57V3, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.2) MUTATED   170  77
  DEL PEAK 33(15Q15.2) WILD-TYPE 278  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.2) MUTATED    170   77
  DEL PEAK 33(15Q15.2) WILD-TYPE  278   85
        clus
vv       DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  COLON                           170                            278
  RECTUM                           77                             85
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 33(15Q15.2) MUTATED        41        0        9        62         3
  DEL PEAK 33(15Q15.2) WILD-TYPE      63        1       28       110         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 33(15Q15.2) MUTATED           1         8          8         35
  DEL PEAK 33(15Q15.2) WILD-TYPE         1        16          7         49
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 33(15Q15.2) MUTATED           27       34        13         2
  DEL PEAK 33(15Q15.2) WILD-TYPE         28       29        11         0
D57V4, multiclass
            clus
vv           DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  STAGE I                              41                             63
  STAGE IA                              0                              1
  STAGE II                              9                             28
  STAGE IIA                            62                            110
  STAGE IIB                             3                              9
  STAGE IIC                             1                              1
  STAGE III                             8                             16
  STAGE IIIA                            8                              7
  STAGE IIIB                           35                             49
  STAGE IIIC                           27                             28
  STAGE IV                             34                             29
  STAGE IVA                            13                             11
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 33(15Q15.2) MUTATED     9  41 175  25
  DEL PEAK 33(15Q15.2) WILD-TYPE  11  64 242  44
D57V5, multiclass
    clus
vv   DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  T1                            9                             11
  T2                           41                             64
  T3                          175                            242
  T4                           25                             44
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 33(15Q15.2) MUTATED   123  75  52
  DEL PEAK 33(15Q15.2) WILD-TYPE 223  75  63
D57V6, multiclass
    clus
vv   DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  N0                          123                            223
  N1                           75                             75
  N2                           52                             63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.2) MUTATED   171  48
  DEL PEAK 33(15Q15.2) WILD-TYPE 282  40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.2) MUTATED    171   48
  DEL PEAK 33(15Q15.2) WILD-TYPE  282   40
   clus
vv  DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  0                          171                            282
  1                           48                             40
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.2) MUTATED   110 140
  DEL PEAK 33(15Q15.2) WILD-TYPE 179 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.2) MUTATED    110  140
  DEL PEAK 33(15Q15.2) WILD-TYPE  179  185
        clus
vv       DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  FEMALE                          110                            179
  MALE                            140                            185
[1] 2 2
[1] FALSE
D57V9, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.2) MUTATED   196  15
  DEL PEAK 33(15Q15.2) WILD-TYPE 286  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.2) MUTATED    196   15
  DEL PEAK 33(15Q15.2) WILD-TYPE  286   14
     clus
vv    DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  NO                           196                            286
  YES                           15                             14
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 33(15Q15.2) MUTATED                    153
  DEL PEAK 33(15Q15.2) WILD-TYPE                  229
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q15.2) MUTATED                              15
  DEL PEAK 33(15Q15.2) WILD-TYPE                            47
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 33(15Q15.2) MUTATED                      70
  DEL PEAK 33(15Q15.2) WILD-TYPE                    76
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 33(15Q15.2) MUTATED                                6
  DEL PEAK 33(15Q15.2) WILD-TYPE                              7
D57V10, multiclass
                                clus
vv                               DEL PEAK 33(15Q15.2) MUTATED
  COLON ADENOCARCINOMA                                    153
  COLON MUCINOUS ADENOCARCINOMA                            15
  RECTAL ADENOCARCINOMA                                    70
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 33(15Q15.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      229
  COLON MUCINOUS ADENOCARCINOMA                              47
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 33(15Q15.2) MUTATED   180   2  16   8
  DEL PEAK 33(15Q15.2) WILD-TYPE 266   4  21  21
D57V11, multiclass
    clus
vv   DEL PEAK 33(15Q15.2) MUTATED DEL PEAK 33(15Q15.2) WILD-TYPE
  R0                          180                            266
  R1                            2                              4
  R2                           16                             21
  RX                            8                             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"
D57V12, continuous
D57V13, binary
                                cls
clus                               0   1
  DEL PEAK 33(15Q15.2) MUTATED     2 143
  DEL PEAK 33(15Q15.2) WILD-TYPE   3 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(15Q15.2) MUTATED      2  143
  DEL PEAK 33(15Q15.2) WILD-TYPE    3  209
                        clus
vv                       DEL PEAK 33(15Q15.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          143
                        clus
vv                       DEL PEAK 33(15Q15.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            209
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 34(15Q21.1) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(15Q21.1) MUTATED   193  47
  DEL PEAK 34(15Q21.1) WILD-TYPE 273  81
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                           240                            354 
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                            47                             81 
$`DEL PEAK 34(15Q21.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       24.33        45.60        37.05        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
       19.99        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 
       12.99        50.99        24.00       106.75        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       63.62        91.79        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 
       25.97        21.24        18.28        26.43         4.80         1.61 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2679 
       39.45        43.76        43.76        43.43        42.90        44.91 
TCGA-A6-2683 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 
       16.57        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-AA-3488 TCGA-AA-3489 TCGA-AA-3494 
       20.12        20.28        61.84         5.03         7.04         1.02 
TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
        6.97         9.07        29.00        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3680 
       21.01        24.00         2.01        50.04        47.01        11.01 
TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
       37.05        38.99        36.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       10.06        33.07        36.03         0.99        31.07        17.03 
TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-A00D 
        2.01        21.99        13.05        34.06        27.02        19.00 
TCGA-AA-A00E TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       30.02        34.03        42.02        17.03        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01K TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02W 
       15.02        31.00        33.04        26.01         2.96        41.00 
TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-5543 
        5.79        22.42        27.42        16.44        14.50        33.01 
TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        0.20        17.85        18.84        65.00        62.79        88.21 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 
       29.56         5.23         3.19        12.46        12.20       148.01 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 TCGA-CM-5862 
        2.01        25.02        27.02        13.02        29.06         5.03 
TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6170 
       15.02        17.03        14.04        29.03        16.04        15.02 
TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       13.05        11.08        11.08        11.01        10.06        12.03 
TCGA-D5-5538 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6898 TCGA-D5-6922 
       54.61        20.19        25.48        15.12         7.53        10.13 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D7 
        9.04        13.41        11.38       130.65        92.75        13.32 
TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A28F TCGA-DM-A28M TCGA-F4-6460 
       12.59       140.38       131.51        35.97        95.18        31.96 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 
       47.87         1.55        43.04        33.67        13.25         0.53 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 
       47.41         8.35        65.85        55.04        61.91        36.00 
TCGA-G4-6322 TCGA-G4-6626 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW 
       26.04        46.75        10.98        19.33        12.79        29.46 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 
       21.90        38.70        11.90        46.92        43.04        13.55 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 
       37.74        29.98        24.59        65.98        11.84        32.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        20.05        24.00        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 
       34.03         6.05        20.98         0.99        29.98        32.98 
TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3901 
        0.99        19.04        19.99        35.01         1.02        25.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 
       19.99        28.04        14.04        13.94        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.02         1.94        38.96        41.00        38.04        38.56 
TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 
       43.20         6.05        13.78        47.44        48.20         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC 
       31.00        13.97        51.98        25.05        25.05        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         3.48         4.18        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        42.35        28.57        32.19        36.49        19.66 

$`DEL PEAK 34(15Q21.1) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       17.95         6.05         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       31.07        24.00         2.01        26.01        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 
       75.95       100.01         1.94        28.21        23.51        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       22.09        35.80        26.17        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
        8.02        15.95        36.03        31.00        51.98        55.76 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2678 TCGA-A6-2680 
       15.62        12.66         9.53        46.65        42.28        35.11 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 TCGA-A6-5661 
       37.05        37.25        37.02        32.75        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-A6-6652 TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6781 
        8.38        25.18        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        56.25         9.63         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 
       35.01        63.98         1.02        38.99         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 
        0.00        29.00        26.01        29.95        20.98        13.94 
TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 
       61.02        78.08         6.97        54.02        14.01        47.05 
TCGA-AA-3679 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       15.02         5.98         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3850 
        0.99        25.02         1.02        17.98        15.95         0.00 
TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 
        0.00        32.05        53.00        27.02        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 
        2.01        24.00        33.01        26.01        20.98        34.03 
TCGA-AA-3971 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       16.08        25.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       18.05        18.05         4.01        27.02         0.99        34.98 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       10.98        32.02        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01S TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02F 
       35.01         1.02         1.02        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5820 
       40.96        12.16        83.24        24.53        26.47         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-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       17.26        19.33       109.28        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-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 
       11.74        12.69        12.36        12.39        12.59        12.59 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.76        10.06        14.30        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       15.62        51.32        21.99        21.14        82.95       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        32.02        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        45.40        19.59        56.09        55.92 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 
       20.42        17.75        18.25        43.27        17.85         4.80 
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        13.35        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 
       35.74        35.74         6.18        34.42        41.42        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 
      133.18        82.39        74.56        67.30        53.62        44.68 
TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50T 
       85.48        39.42        26.43        13.78        74.79        18.18 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       19.33         9.93        15.65        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2689 TCGA-AF-2690 
        8.42        31.30        60.13        70.03        39.48        17.23 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       37.97        34.49        16.83        24.36        20.02        86.63 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
       36.03        12.00         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        37.02 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        0.99         1.02        17.95        36.95        13.02        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       48.03        32.02        36.03         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N 
       20.98         6.02         9.07         1.02        49.97        61.97 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 
        2.50        27.55        26.43        19.46        33.17        44.78 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
       78.12        21.01        25.05        26.04        12.00        31.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       10.98        44.02        25.97        12.62       126.44       129.27 
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-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       17.69        16.34        17.46         8.45         9.96        49.51 
TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
        0.39        37.18        38.14        11.87        12.46        47.08 

  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                             0                              0 
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                        148.01                         139.17 
  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE 
                        24.000                         21.255 
[1] "0.0 - 148.0 (24.0)" "0.0 - 139.2 (21.3)"
[1] "hr=" "1.2"
D58V2, continuous
D58V3, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q21.1) MUTATED   168  77
  DEL PEAK 34(15Q21.1) WILD-TYPE 280  85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q21.1) MUTATED    168   77
  DEL PEAK 34(15Q21.1) WILD-TYPE  280   85
        clus
vv       DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  COLON                           168                            280
  RECTUM                           77                             85
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 34(15Q21.1) MUTATED        38        0        9        65         4
  DEL PEAK 34(15Q21.1) WILD-TYPE      66        1       28       107         8
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(15Q21.1) MUTATED           1         8          8         33
  DEL PEAK 34(15Q21.1) WILD-TYPE         1        16          7         51
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 34(15Q21.1) MUTATED           26       33        13         2
  DEL PEAK 34(15Q21.1) WILD-TYPE         29       30        11         0
D58V4, multiclass
            clus
vv           DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  STAGE I                              38                             66
  STAGE IA                              0                              1
  STAGE II                              9                             28
  STAGE IIA                            65                            107
  STAGE IIB                             4                              8
  STAGE IIC                             1                              1
  STAGE III                             8                             16
  STAGE IIIA                            8                              7
  STAGE IIIB                           33                             51
  STAGE IIIC                           26                             29
  STAGE IV                             33                             30
  STAGE IVA                            13                             11
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 34(15Q21.1) MUTATED     8  39 174  26
  DEL PEAK 34(15Q21.1) WILD-TYPE  12  66 243  43
D58V5, multiclass
    clus
vv   DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  T1                            8                             12
  T2                           39                             66
  T3                          174                            243
  T4                           26                             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 34(15Q21.1) MUTATED   124  72  51
  DEL PEAK 34(15Q21.1) WILD-TYPE 222  78  64
D58V6, multiclass
    clus
vv   DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  N0                          124                            222
  N1                           72                             78
  N2                           51                             64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q21.1) MUTATED   170  47
  DEL PEAK 34(15Q21.1) WILD-TYPE 283  41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q21.1) MUTATED    170   47
  DEL PEAK 34(15Q21.1) WILD-TYPE  283   41
   clus
vv  DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  0                          170                            283
  1                           47                             41
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q21.1) MUTATED   107 140
  DEL PEAK 34(15Q21.1) WILD-TYPE 182 185
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q21.1) MUTATED    107  140
  DEL PEAK 34(15Q21.1) WILD-TYPE  182  185
        clus
vv       DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  FEMALE                          107                            182
  MALE                            140                            185
[1] 2 2
[1] FALSE
D58V9, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q21.1) MUTATED   192  15
  DEL PEAK 34(15Q21.1) WILD-TYPE 290  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q21.1) MUTATED    192   15
  DEL PEAK 34(15Q21.1) WILD-TYPE  290   14
     clus
vv    DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  NO                           192                            290
  YES                           15                             14
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 34(15Q21.1) MUTATED                    151
  DEL PEAK 34(15Q21.1) WILD-TYPE                  231
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(15Q21.1) MUTATED                              15
  DEL PEAK 34(15Q21.1) WILD-TYPE                            47
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 34(15Q21.1) MUTATED                      70
  DEL PEAK 34(15Q21.1) WILD-TYPE                    76
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 34(15Q21.1) MUTATED                                6
  DEL PEAK 34(15Q21.1) WILD-TYPE                              7
D58V10, multiclass
                                clus
vv                               DEL PEAK 34(15Q21.1) MUTATED
  COLON ADENOCARCINOMA                                    151
  COLON MUCINOUS ADENOCARCINOMA                            15
  RECTAL ADENOCARCINOMA                                    70
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 34(15Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      231
  COLON MUCINOUS ADENOCARCINOMA                              47
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 34(15Q21.1) MUTATED   178   1  16   8
  DEL PEAK 34(15Q21.1) WILD-TYPE 268   5  21  21
D58V11, multiclass
    clus
vv   DEL PEAK 34(15Q21.1) MUTATED DEL PEAK 34(15Q21.1) WILD-TYPE
  R0                          178                            268
  R1                            1                              5
  R2                           16                             21
  RX                            8                             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"
D58V12, continuous
D58V13, binary
                                cls
clus                               0   1
  DEL PEAK 34(15Q21.1) MUTATED     2 137
  DEL PEAK 34(15Q21.1) WILD-TYPE   3 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(15Q21.1) MUTATED      2  137
  DEL PEAK 34(15Q21.1) WILD-TYPE    3  215
                        clus
vv                       DEL PEAK 34(15Q21.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          137
                        clus
vv                       DEL PEAK 34(15Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            215
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 35(15Q22.33) MUTATION ANALYSIS
D59V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 35(15Q22.33) MUTATED   184  46
  DEL PEAK 35(15Q22.33) WILD-TYPE 282  82
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                            230                             364 
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                             46                              82 
$`DEL PEAK 35(15Q22.33) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-AA-3522 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       24.33        45.60        37.05        13.02        23.01        19.99 
TCGA-AA-3562 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
       19.99        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3979 TCGA-AZ-4681 TCGA-CK-5912 TCGA-DM-A285 
       12.99        50.99        24.00       106.75        49.08         5.88 
TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       63.62        91.79        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 
       25.97        21.24        18.28        26.43         4.80         1.61 
TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2679 TCGA-A6-2683 
       39.45        43.76        43.76        43.43        44.91        16.57 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5667 
       34.65        36.53        32.45        30.44        29.19        29.16 
TCGA-A6-6138 TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6782 TCGA-A6-A567 
       22.52        25.08        20.61        21.76        20.28        61.84 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3511 TCGA-AA-3519 TCGA-AA-3532 
        5.03         7.04         1.02         6.97         9.07        29.00 
TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 
       12.99        33.99        21.01         2.01        50.04        37.05 
TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3856 
       38.99        36.95        37.02        17.03        10.06         0.99 
TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 TCGA-AA-3975 
       31.07        17.03         2.01        21.99        13.05        34.06 
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-AM-5820 
       41.00         5.79        22.42        27.42        16.44         0.46 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D 
       14.50        16.31         0.95        33.01         0.20        17.85 
TCGA-AY-A8YK TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6603 TCGA-AZ-6605 
       18.84        65.00        62.79        88.21        29.56         5.23 
TCGA-AZ-6607 TCGA-CA-5256 TCGA-CA-6716 TCGA-CK-4948 TCGA-CK-6748 TCGA-CM-4747 
        3.19        12.46        12.20       148.01         2.01        25.02 
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-6676 TCGA-CM-6677 
       14.04        29.03        16.04        15.02        11.08        11.08 
TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6535 
       11.01        10.06        12.03        20.19        25.48        15.12 
TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6926 TCGA-D5-6929 
       17.13        12.49         7.53        10.13         9.04        13.41 
TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 
       11.38       130.65        92.75        49.91        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1HA TCGA-DM-A288 TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6703 
      140.38       131.51        14.04        95.18        31.96        47.87 
TCGA-F4-6704 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
        1.55        43.04        33.67        13.25         0.53        47.41 
TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 
        8.35        65.85        55.04        61.91        36.00        46.75 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-QG-A5YW TCGA-QG-A5Z1 TCGA-QL-A97D 
       10.98        19.33        12.79        29.46         8.42        21.90 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       38.70        11.90        46.92        43.04        13.55        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 
       37.74        29.98        24.59        65.98        32.02        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3608 
       20.05        24.00        34.03        34.03         6.05        15.95 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3893 
       20.98        29.98         0.99        19.04        19.99        35.01 
TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-A008 
        1.02        25.02        19.99        28.04        14.04        13.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       23.01        37.02         1.02        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-CL-5918 
       38.56        43.20         6.05        13.78        47.44         7.17 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
       21.01        31.00        13.97        51.98        25.05        25.05 
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         3.48 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        4.18        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        42.35        28.57        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6864 
       19.66        12.46 

$`DEL PEAK 35(15Q22.33) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 
       13.94        14.53        24.16         1.02        58.03        13.02 
TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       24.03        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       17.95         6.05         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L 
       31.07        24.00         2.01        26.01        19.07        38.04 
TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 
       21.99        39.06        21.37        15.52        25.08        10.88 
TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 
       75.95       100.01         1.94        28.21        23.51        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 
       22.09        35.80        26.17        79.69        17.85        10.39 
TCGA-AG-3580 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
        8.02        15.95        36.03        31.00        51.98        55.76 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2678 
       15.62        12.66         9.53        46.65        42.90        42.28 
TCGA-A6-2680 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5656 
       35.11        37.05        37.25        37.02        32.75        32.91 
TCGA-A6-5657 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       31.63        33.53        23.61        22.09        22.06        32.71 
TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6653 
       27.09        24.13         8.38        25.18        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        56.25 
TCGA-A6-A5ZU TCGA-AA-3492 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
        9.63         3.02        37.05        35.01        63.98         1.02 
TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3538 
       38.99         1.02        19.07         0.00        29.00        26.01 
TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       14.01        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
       78.08         6.97        54.02        14.01        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       15.02        11.01         5.98         5.03        26.99        10.06 
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-3845 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
        0.00         0.00        33.07         0.00        36.03        32.05 
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-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3977 
       33.01        26.01        20.98        34.03        16.08        25.02 
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-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01D 
       18.05         4.01        27.02         0.99        34.98        10.98 
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-A029 TCGA-AA-A02F TCGA-AA-A02H 
        1.02         1.02        37.02        51.98        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 
       12.16        83.24        24.53        26.47         0.92        27.09 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AZ-4308 TCGA-AZ-4315 
       21.44        17.82        17.26        19.33       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-6598 
        1.41         5.65        32.94         5.13        22.36        49.41 
TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5796 
        6.77        12.10        11.74        12.69        12.36        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.59        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
       82.95       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        32.02        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-CM-6675 TCGA-D5-5537 
       13.02        14.04        11.01        12.95        13.05        45.40 
TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 
       54.61        19.59        56.09        55.92        20.42        17.75 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 
       18.25        43.27        17.85         4.80        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        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1DA 
       12.00        10.26       119.70        24.43        38.20         7.50 
TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A28A TCGA-DM-A28C 
       44.32       135.65         7.76       139.17        26.47        81.37 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-F4-6459 
      119.93        35.97        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        35.74        35.74         6.18        34.42        41.42 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       35.31       133.18        82.39        74.56        67.30        53.62 
TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 
       44.68        85.48        39.42        26.43        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A8F8 
       74.79        18.18        19.33         9.93        15.65        16.80 
TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z2 TCGA-SS-A7HO TCGA-WS-AB45 TCGA-AF-2689 
       42.77        32.98        31.30        60.13        70.03        39.48 
TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       17.23        37.97        16.83        24.36        20.02        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3587 
       11.84        36.03        12.00         7.07         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 
       34.03         2.01        50.04        12.03         0.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 
        7.99         0.99        37.02        32.98         0.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.95        36.95        13.02        14.01        48.03        32.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       36.03         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AH-6547 
        9.07         1.02        49.97         1.94        61.97         2.50 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
       27.55        26.43        19.46        33.17        44.78        48.20 
TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       78.12        25.05        26.04        12.00        31.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6506 
       44.02        25.97        12.62       126.44        32.61        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-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
        8.61        17.46         8.45         9.96        49.51         0.39 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       37.18        38.14        11.87        47.08 

  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                         148.01                          139.17 
  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE 
                         21.945                          22.030 
[1] "0.2 - 148.0 (21.9)" "0.0 - 139.2 (22.0)"
[1] "hr=" "1.1"
D59V2, continuous
D59V3, binary
                                 cls
clus                                0   1
  DEL PEAK 35(15Q22.33) MUTATED   159  75
  DEL PEAK 35(15Q22.33) WILD-TYPE 289  87
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(15Q22.33) MUTATED    159   75
  DEL PEAK 35(15Q22.33) WILD-TYPE  289   87
        clus
vv       DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  COLON                            159                             289
  RECTUM                            75                              87
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 35(15Q22.33) MUTATED        32        0        8        62         3
  DEL PEAK 35(15Q22.33) WILD-TYPE      72        1       29       110         9
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(15Q22.33) MUTATED           1         6          8         34
  DEL PEAK 35(15Q22.33) WILD-TYPE         1        18          7         50
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 35(15Q22.33) MUTATED           28       32        14         1
  DEL PEAK 35(15Q22.33) WILD-TYPE         27       31        10         1
D59V4, multiclass
            clus
vv           DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  STAGE I                               32                              72
  STAGE IA                               0                               1
  STAGE II                               8                              29
  STAGE IIA                             62                             110
  STAGE IIB                              3                               9
  STAGE IIC                              1                               1
  STAGE III                              6                              18
  STAGE IIIA                             8                               7
  STAGE IIIB                            34                              50
  STAGE IIIC                            28                              27
  STAGE IV                              32                              31
  STAGE IVA                             14                              10
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 35(15Q22.33) MUTATED     9  31 174  23
  DEL PEAK 35(15Q22.33) WILD-TYPE  11  74 243  46
D59V5, multiclass
    clus
vv   DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  T1                             9                              11
  T2                            31                              74
  T3                           174                             243
  T4                            23                              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 35(15Q22.33) MUTATED   114  69  54
  DEL PEAK 35(15Q22.33) WILD-TYPE 232  81  61
D59V6, multiclass
    clus
vv   DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  N0                           114                             232
  N1                            69                              81
  N2                            54                              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"
D59V7, binary
                                 cls
clus                                0   1
  DEL PEAK 35(15Q22.33) MUTATED   161  46
  DEL PEAK 35(15Q22.33) WILD-TYPE 292  42
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(15Q22.33) MUTATED    161   46
  DEL PEAK 35(15Q22.33) WILD-TYPE  292   42
   clus
vv  DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  0                           161                             292
  1                            46                              42
[1] 2 2
[1] FALSE
D59V8, binary
                                 cls
clus                                0   1
  DEL PEAK 35(15Q22.33) MUTATED   105 132
  DEL PEAK 35(15Q22.33) WILD-TYPE 184 193
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(15Q22.33) MUTATED    105  132
  DEL PEAK 35(15Q22.33) WILD-TYPE  184  193
        clus
vv       DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  FEMALE                           105                             184
  MALE                             132                             193
[1] 2 2
[1] FALSE
D59V9, binary
                                 cls
clus                                0   1
  DEL PEAK 35(15Q22.33) MUTATED   184  14
  DEL PEAK 35(15Q22.33) WILD-TYPE 298  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(15Q22.33) MUTATED    184   14
  DEL PEAK 35(15Q22.33) WILD-TYPE  298   15
     clus
vv    DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  NO                            184                             298
  YES                            14                              15
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 35(15Q22.33) MUTATED                    143
  DEL PEAK 35(15Q22.33) WILD-TYPE                  239
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(15Q22.33) MUTATED                              14
  DEL PEAK 35(15Q22.33) WILD-TYPE                            48
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 35(15Q22.33) MUTATED                      68
  DEL PEAK 35(15Q22.33) WILD-TYPE                    78
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 35(15Q22.33) MUTATED                                6
  DEL PEAK 35(15Q22.33) WILD-TYPE                              7
D59V10, multiclass
                                clus
vv                               DEL PEAK 35(15Q22.33) MUTATED
  COLON ADENOCARCINOMA                                     143
  COLON MUCINOUS ADENOCARCINOMA                             14
  RECTAL ADENOCARCINOMA                                     68
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 35(15Q22.33) WILD-TYPE
  COLON ADENOCARCINOMA                                       239
  COLON MUCINOUS ADENOCARCINOMA                               48
  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"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 35(15Q22.33) MUTATED   170   1  15   8
  DEL PEAK 35(15Q22.33) WILD-TYPE 276   5  22  21
D59V11, multiclass
    clus
vv   DEL PEAK 35(15Q22.33) MUTATED DEL PEAK 35(15Q22.33) WILD-TYPE
  R0                           170                             276
  R1                             1                               5
  R2                            15                              22
  RX                             8                              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"
D59V12, continuous
D59V13, binary
                                 cls
clus                                0   1
  DEL PEAK 35(15Q22.33) MUTATED     2 139
  DEL PEAK 35(15Q22.33) WILD-TYPE   3 213
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(15Q22.33) MUTATED      2  139
  DEL PEAK 35(15Q22.33) WILD-TYPE    3  213
                        clus
vv                       DEL PEAK 35(15Q22.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                           139
                        clus
vv                       DEL PEAK 35(15Q22.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             213
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 36(16P13.3) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(16P13.3) MUTATED    46  20
  DEL PEAK 36(16P13.3) WILD-TYPE 420 108
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            66                            528 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                            20                            108 
$`DEL PEAK 36(16P13.3) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-AA-3552 TCGA-AA-3860 TCGA-AA-3952 
       24.33        45.60        14.53        13.02        31.07         2.01 
TCGA-G4-6294 TCGA-G5-6233 TCGA-A6-2679 TCGA-A6-3807 TCGA-A6-6651 TCGA-A6-A567 
       28.21        18.28        44.91        34.65        21.76        61.84 
TCGA-AA-3488 TCGA-AA-3664 TCGA-AA-3685 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3930 
        5.03        54.02        37.05        38.99        36.95         2.01 
TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3982 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A02F 
       33.01         2.01        27.02        34.03        27.02        39.98 
TCGA-AA-A02Y TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 
       39.98        16.44         0.46        14.50        16.31         0.20 
TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-6607 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 
       17.85         5.65         3.19        13.02        22.03        22.98 
TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6165 TCGA-CM-6169 TCGA-CM-6172 TCGA-CM-6678 
        5.03        15.02        16.04        13.02        11.01        11.01 
TCGA-D5-6529 TCGA-D5-6531 TCGA-DM-A1D6 TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-F4-6459 
       20.19        17.75        49.91        12.59        44.32         8.61 
TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5YV TCGA-RU-A8FL TCGA-T9-A92H 
       46.75        18.18        10.98        42.77        38.70        11.90 
TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3881 
       32.02        34.03         6.05        19.99         7.99        19.04 
TCGA-AG-4005 TCGA-AG-A02G TCGA-DC-6682 TCGA-EI-6882 TCGA-F5-6811 TCGA-F5-6814 
       14.04        38.96        25.05         8.61        32.19        37.18 

$`DEL PEAK 36(16P13.3) WILD-TYPE`
TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       13.94        24.16         1.02        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 
       37.05        36.03         8.05        19.07        34.03         0.99 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 
       17.95        23.01        19.99        19.99         6.05         0.92 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 
       24.03        29.98        12.99        24.00        50.99        26.01 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94        49.08         5.88        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 
       55.76        26.43        15.62         4.80        12.66         1.61 
TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
        9.53        39.45        43.76        46.65        43.76        43.43 
TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.90        42.28        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5665 
       30.44        29.19        33.53        23.61        22.09        22.06 
TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6141 
       32.71        29.16        27.09        22.52        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        25.18        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        56.25 
TCGA-A6-A5ZU TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 
        9.63         7.04         3.02         1.02        37.05        35.01 
TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3519 
       63.98         6.97         1.02        38.99         1.02         9.07 
TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 
       19.07         0.00        29.00        29.00        26.01        12.99 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       14.01        33.99        21.01        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3666 TCGA-AA-3667 
       13.94        61.02        78.08         6.97         2.01        14.01 
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-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 
        5.03        26.99        10.06        35.05         0.99        25.02 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 
        1.02        17.98        15.95        37.02         0.00        17.03 
TCGA-AA-3848 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 
       10.06         0.00        33.07         0.00        36.03        32.05 
TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 
        0.99        31.07        53.00        17.03        27.02        18.05 
TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       31.00        24.00        26.01        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3989 TCGA-AA-3994 
       16.08        13.05        34.06        25.02         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-A00N TCGA-AA-A00Q TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 
        4.01        42.02         0.99        17.03        14.99        34.98 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01I 
       15.02        15.02        10.98        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-A029 TCGA-AA-A02E TCGA-AA-A02H 
        1.02        26.01        37.02        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02W TCGA-AA-A03F TCGA-AA-A03J 
        5.03         0.92        22.03        41.00        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-6965 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
       26.47         0.92        27.09         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 
       17.82        17.26        19.33        18.84       109.28        58.39 
TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
        1.41        32.94         5.13        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-5797 
       11.74        12.69        12.36        12.46        12.39        12.59 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         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        25.02        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        32.02        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        45.40        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.42        18.25        25.48        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        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        13.35        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-A288 TCGA-DM-A28A TCGA-DM-A28C TCGA-DM-A28E TCGA-DM-A28F 
      139.17        14.04        26.47        81.37       119.93        35.97 
TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
       60.79       117.07        98.24        95.18        31.96        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 
       35.74        35.74         6.18        47.87         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       41.42        43.04        33.67        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       35.31       133.18         8.35        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 
       61.91        36.00        26.43        26.04        13.78        74.79 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        21.90        60.13 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        20.98         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       25.02        32.02        19.99        28.04        36.03         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       51.98        10.98        44.02        25.97        25.05        12.62 
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         3.48         4.18        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-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.41        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-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        38.14        11.87        12.46        47.08 

  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                         61.84                         148.01 
  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE 
                        19.515                         22.090 
[1] "0.2 - 61.8 (19.5)"  "0.0 - 148.0 (22.1)"
[1] "hr=" "1.9"
D60V2, continuous
D60V3, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P13.3) MUTATED    55  13
  DEL PEAK 36(16P13.3) WILD-TYPE 393 149
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED     55   13
  DEL PEAK 36(16P13.3) WILD-TYPE  393  149
        clus
vv       DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  COLON                            55                            393
  RECTUM                           13                            149
[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        24         2
  DEL PEAK 36(16P13.3) WILD-TYPE     100        1       34       148        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 36(16P13.3) MUTATED           0         0          0          9
  DEL PEAK 36(16P13.3) WILD-TYPE         2        24         15         75
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 36(16P13.3) MUTATED           11        8         5         0
  DEL PEAK 36(16P13.3) WILD-TYPE         44       55        19         2
D60V4, multiclass
            clus
vv           DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  STAGE I                               4                            100
  STAGE IA                              0                              1
  STAGE II                              3                             34
  STAGE IIA                            24                            148
  STAGE IIB                             2                             10
  STAGE IIC                             0                              2
  STAGE III                             0                             24
  STAGE IIIA                            0                             15
  STAGE IIIB                            9                             75
  STAGE IIIC                           11                             44
  STAGE IV                              8                             55
  STAGE IVA                             5                             19
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 36(16P13.3) MUTATED     0   5  56   7
  DEL PEAK 36(16P13.3) WILD-TYPE  20 100 361  62
D60V5, multiclass
    clus
vv   DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  T1                            0                             20
  T2                            5                            100
  T3                           56                            361
  T4                            7                             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 36(16P13.3) MUTATED    34  16  18
  DEL PEAK 36(16P13.3) WILD-TYPE 312 134  97
D60V6, multiclass
    clus
vv   DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  N0                           34                            312
  N1                           16                            134
  N2                           18                             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"
D60V7, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P13.3) MUTATED    46  13
  DEL PEAK 36(16P13.3) WILD-TYPE 407  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED     46   13
  DEL PEAK 36(16P13.3) WILD-TYPE  407   75
   clus
vv  DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  0                           46                            407
  1                           13                             75
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P13.3) MUTATED    30  38
  DEL PEAK 36(16P13.3) WILD-TYPE 259 287
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED     30   38
  DEL PEAK 36(16P13.3) WILD-TYPE  259  287
        clus
vv       DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  FEMALE                           30                            259
  MALE                             38                            287
[1] 2 2
[1] FALSE
D60V9, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P13.3) MUTATED    56   2
  DEL PEAK 36(16P13.3) WILD-TYPE 426  27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED     56    2
  DEL PEAK 36(16P13.3) WILD-TYPE  426   27
     clus
vv    DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  NO                            56                            426
  YES                            2                             27
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 36(16P13.3) MUTATED                     48
  DEL PEAK 36(16P13.3) WILD-TYPE                  334
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(16P13.3) MUTATED                               7
  DEL PEAK 36(16P13.3) WILD-TYPE                            55
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 36(16P13.3) MUTATED                      10
  DEL PEAK 36(16P13.3) WILD-TYPE                   136
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 36(16P13.3) MUTATED                                2
  DEL PEAK 36(16P13.3) WILD-TYPE                             11
D60V10, multiclass
                                clus
vv                               DEL PEAK 36(16P13.3) MUTATED
  COLON ADENOCARCINOMA                                     48
  COLON MUCINOUS ADENOCARCINOMA                             7
  RECTAL ADENOCARCINOMA                                    10
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 36(16P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      334
  COLON MUCINOUS ADENOCARCINOMA                              55
  RECTAL ADENOCARCINOMA                                     136
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 36(16P13.3) MUTATED    51   1   4   1
  DEL PEAK 36(16P13.3) WILD-TYPE 395   5  33  28
D60V11, multiclass
    clus
vv   DEL PEAK 36(16P13.3) MUTATED DEL PEAK 36(16P13.3) WILD-TYPE
  R0                           51                            395
  R1                            1                              5
  R2                            4                             33
  RX                            1                             28
[1] 4 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
D60V13, binary
                                cls
clus                               0   1
  DEL PEAK 36(16P13.3) MUTATED     1  41
  DEL PEAK 36(16P13.3) WILD-TYPE   4 311
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(16P13.3) MUTATED      1   41
  DEL PEAK 36(16P13.3) WILD-TYPE    4  311
                        clus
vv                       DEL PEAK 36(16P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       DEL PEAK 36(16P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            311
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 37(16Q23.1) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(16Q23.1) MUTATED    62  20
  DEL PEAK 37(16Q23.1) WILD-TYPE 404 108
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            82                            512 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                            20                            108 
$`DEL PEAK 37(16Q23.1) MUTATED`
TCGA-A6-2681 TCGA-AA-3516 TCGA-AA-3543 TCGA-AA-3672 TCGA-AA-3860 TCGA-G5-6233 
       45.60        13.02         0.99         0.92        31.07        18.28 
TCGA-5M-AAT4 TCGA-A6-2671 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-5660 TCGA-A6-5661 
        1.61        43.76        42.90        42.28        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-3518 TCGA-AA-3549 TCGA-AA-3685 TCGA-AA-3831 TCGA-AA-3837 
        6.97         1.02        21.01        37.05        17.98        38.99 
TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3947 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-A00E 
       36.03        53.00        33.01         2.01        21.99        30.02 
TCGA-AA-A00J TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A02E TCGA-AA-A02R TCGA-AA-A02W 
       18.05        38.07         1.02         2.96        22.03        41.00 
TCGA-AD-A5EK TCGA-AY-A69D TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6598 TCGA-AZ-6600 
       16.44        17.85         5.65         5.13        49.41        12.10 
TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5797 TCGA-CM-5344 TCGA-CM-5862 TCGA-CM-5863 
        3.19        12.69        12.59        22.03         5.03        15.02 
TCGA-CM-6169 TCGA-CM-6678 TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6535 TCGA-DM-A0XD 
       13.02        11.01        20.19        17.75        15.12        24.43 
TCGA-DM-A1DA TCGA-NH-A50T TCGA-NH-A50U TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-T9-A92H 
        7.50        18.18        10.98        31.30        38.70        11.90 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-3609 
       24.59        32.02        36.03        34.03         6.05        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-4005 
       20.98         7.99        32.98        19.04         1.02        14.04 
TCGA-AH-6544 TCGA-AH-6644 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6883 TCGA-EI-7002 
       38.56        27.55        25.05       129.27        11.51        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6811 TCGA-F5-6814 
        8.45         9.96        32.19        37.18 

$`DEL PEAK 37(16Q23.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        13.94        14.53        24.16         1.02        58.03 
TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       24.03        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 
       13.02        17.95        23.01        19.99        19.99         6.05 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
       19.00        36.00        85.05        19.04        19.04        14.93 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       26.01        24.00        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      100.01         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 
       63.62        35.93        22.09        35.80        26.17        91.79 
TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       79.69        17.85        10.39         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       17.03        17.03        25.97        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       51.98        21.24        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 
       12.66         9.53        39.45        46.65        43.76        43.43 
TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 
       44.91        35.11        16.57        37.05        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        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-A6-6650 TCGA-A6-6652 
       24.13         8.38        25.08        25.18        20.61        24.69 
TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A566 TCGA-A6-A567 
       23.87        20.12        19.66        20.28        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3495 
       56.25         9.63         5.03         7.04         3.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 
       35.01        63.98         1.02        38.99         9.07        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        0.00        29.00        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 
       33.99        24.00        29.95        20.98        13.94        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 
       78.08         6.97        54.02         2.01        14.01        50.04 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 
       26.99        10.06        35.05         0.99        25.02         1.02 
TCGA-AA-3833 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        36.95        37.02         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 
        0.00        33.07         0.00        32.05         0.99        31.07 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       26.01        20.98        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       25.02        27.02         7.96        27.02        13.94        38.04 
TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00Q 
       19.00        34.03        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-A01F TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01R 
       10.98        32.02        12.00        31.00        31.00        35.01 
TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A029 
        1.02        33.04         1.02        26.01        37.02        51.98 
TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02Y TCGA-AA-A03F 
       39.98         2.01         5.03         0.92        39.98        18.05 
TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
       40.96        12.16        83.24        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 
       27.42        26.47         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        33.01         0.20        21.44        17.82 
TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.26        19.33        18.84       109.28        58.39         1.41 
TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6599 
       32.94        22.36        65.00        62.79        88.21         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       29.56         5.23        11.74        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 
      148.01        85.45        70.16        15.62        51.32        21.99 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       21.14        82.95         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        25.02        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        32.02        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-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 
       45.40        54.61        19.59        56.09        55.92        20.42 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        25.48        43.27        17.85         4.80        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 
       13.35        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-A288 
       44.32       131.51       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-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 
       98.24        95.18         8.61        31.96        11.11        35.74 
TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 
       35.74         6.18        47.87         1.55        34.42        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 
       43.04        33.67        13.25         0.53        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 
      133.18         8.35        82.39        74.56        67.30        65.85 
TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 
       53.62        44.68        55.04        85.48        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 
       36.00        26.43        26.04        13.78        46.75        74.79 
TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       19.33        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-SS-A7HO 
       42.77        29.46        32.98         8.42        21.90        60.13 
TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       70.03        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       37.97        34.49        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
        7.07        20.05        24.00         1.02        46.03        34.03 
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-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98        37.02         0.99         0.99        19.99 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
        1.94        38.96        61.97        41.00        38.04         2.50 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       43.20        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       51.98        10.98        44.02        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        3.48         4.18        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-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 
        8.61        10.78        13.64        17.46        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
       28.57         0.39        36.49        19.66        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                          0.92                           0.00 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                        129.27                         148.01 
  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE 
                        19.515                         23.010 
[1] "0.9 - 129.3 (19.5)" "0.0 - 148.0 (23.0)"
[1] "hr=" "1.6"
D61V2, continuous
D61V3, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    60  23
  DEL PEAK 37(16Q23.1) WILD-TYPE 388 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     60   23
  DEL PEAK 37(16Q23.1) WILD-TYPE  388  139
        clus
vv       DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  COLON                            60                            388
  RECTUM                           23                            139
[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        25         2
  DEL PEAK 37(16Q23.1) WILD-TYPE      91        1       32       147        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 37(16Q23.1) MUTATED           1         4          0          8
  DEL PEAK 37(16Q23.1) WILD-TYPE         1        20         15         76
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 37(16Q23.1) MUTATED            6       11         4         0
  DEL PEAK 37(16Q23.1) WILD-TYPE         49       52        20         2
D61V4, multiclass
            clus
vv           DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  STAGE I                              13                             91
  STAGE IA                              0                              1
  STAGE II                              5                             32
  STAGE IIA                            25                            147
  STAGE IIB                             2                             10
  STAGE IIC                             1                              1
  STAGE III                             4                             20
  STAGE IIIA                            0                             15
  STAGE IIIB                            8                             76
  STAGE IIIC                            6                             49
  STAGE IV                             11                             52
  STAGE IVA                             4                             20
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 37(16Q23.1) MUTATED     0  13  58  12
  DEL PEAK 37(16Q23.1) WILD-TYPE  20  92 359  57
D61V5, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  T1                            0                             20
  T2                           13                             92
  T3                           58                            359
  T4                           12                             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 37(16Q23.1) MUTATED    49  16  17
  DEL PEAK 37(16Q23.1) WILD-TYPE 297 134  98
D61V6, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  N0                           49                            297
  N1                           16                            134
  N2                           17                             98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    58  15
  DEL PEAK 37(16Q23.1) WILD-TYPE 395  73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     58   15
  DEL PEAK 37(16Q23.1) WILD-TYPE  395   73
   clus
vv  DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  0                           58                            395
  1                           15                             73
[1] 2 2
[1] FALSE
D61V8, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    42  41
  DEL PEAK 37(16Q23.1) WILD-TYPE 247 284
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     42   41
  DEL PEAK 37(16Q23.1) WILD-TYPE  247  284
        clus
vv       DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  FEMALE                           42                            247
  MALE                             41                            284
[1] 2 2
[1] FALSE
D61V9, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED    68   4
  DEL PEAK 37(16Q23.1) WILD-TYPE 414  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED     68    4
  DEL PEAK 37(16Q23.1) WILD-TYPE  414   25
     clus
vv    DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  NO                            68                            414
  YES                            4                             25
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                     50
  DEL PEAK 37(16Q23.1) WILD-TYPE                  332
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                              10
  DEL PEAK 37(16Q23.1) WILD-TYPE                            52
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                      20
  DEL PEAK 37(16Q23.1) WILD-TYPE                   126
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 37(16Q23.1) MUTATED                                2
  DEL PEAK 37(16Q23.1) WILD-TYPE                             11
D61V10, multiclass
                                clus
vv                               DEL PEAK 37(16Q23.1) MUTATED
  COLON ADENOCARCINOMA                                     50
  COLON MUCINOUS ADENOCARCINOMA                            10
  RECTAL ADENOCARCINOMA                                    20
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 37(16Q23.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      332
  COLON MUCINOUS ADENOCARCINOMA                              52
  RECTAL ADENOCARCINOMA                                     126
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 37(16Q23.1) MUTATED    58   0   3   4
  DEL PEAK 37(16Q23.1) WILD-TYPE 388   6  34  25
D61V11, multiclass
    clus
vv   DEL PEAK 37(16Q23.1) MUTATED DEL PEAK 37(16Q23.1) WILD-TYPE
  R0                           58                            388
  R1                            0                              6
  R2                            3                             34
  RX                            4                             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"
D61V12, continuous
D61V13, binary
                                cls
clus                               0   1
  DEL PEAK 37(16Q23.1) MUTATED     2  44
  DEL PEAK 37(16Q23.1) WILD-TYPE   3 308
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(16Q23.1) MUTATED      2   44
  DEL PEAK 37(16Q23.1) WILD-TYPE    3  308
                        clus
vv                       DEL PEAK 37(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           44
                        clus
vv                       DEL PEAK 37(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            308
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 38(17P12) MUTATION ANALYSIS
D62V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 38(17P12) MUTATED   276  78
  DEL PEAK 38(17P12) WILD-TYPE 190  50
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                         354                          240 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                          78                           50 
$`DEL PEAK 38(17P12) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        14.53        24.16         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       37.05        36.03        13.02        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3867 TCGA-AA-3870 
        6.05        19.00        36.00        85.05        24.03        29.98 
TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L TCGA-AA-A00Z 
        2.01        50.99        26.01        24.00        38.04        21.99 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 
       21.37        15.52       106.75         1.94        49.08         5.88 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AG-3611 
       23.51        63.62        35.93        91.79        17.85        13.94 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        25.97        15.95        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE 
       21.24        55.76        15.62         4.80         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2680 TCGA-A6-2683 
       43.76        43.76        43.43        42.28        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-3807 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.05        37.25        34.65        32.45        32.91        31.63 
TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6138 
       30.44        29.19        32.71        29.16        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6652 TCGA-A6-6654 TCGA-A6-6782 
       24.13        25.18        20.61        24.69        23.87        20.28 
TCGA-A6-A567 TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 
       61.84         5.03         7.04         1.02        37.05         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3542 TCGA-AA-3544 
        1.02        38.99         9.07        29.00        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       33.99        21.01        24.00        13.94        61.02        78.08 
TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3681 TCGA-AA-3685 
        2.01        14.01        50.04        47.01         5.98        37.05 
TCGA-AA-3811 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3848 
       10.06        25.02        38.99        36.95        37.02        10.06 
TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       33.07        32.05         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       18.05         2.01        24.00        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F 
       16.08        34.06        27.02         7.96        19.00        34.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01D 
       27.02        42.02        17.03        14.99        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01G TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01Z 
       32.02        12.00        31.00         1.02        33.04        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J 
        2.96        39.98         2.01         5.03        41.00        40.96 
TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK 
       24.53         5.79        22.42        27.42        26.47        16.44 
TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6196 
        0.46        14.50        16.31         0.95        33.01         0.20 
TCGA-AY-A69D TCGA-AZ-4308 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 
       17.85       109.28         1.41         5.65         5.13        22.36 
TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
       65.00        88.21        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 
       12.69        12.46        12.59        12.59        12.20        14.30 
TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 
      148.01        21.99         2.01        25.02         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        45.40        54.61 
TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 
       19.59        56.09        55.92        17.75        18.25        25.48 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 
       43.27        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-A288 TCGA-DM-A28A 
      140.38        44.32       131.51       139.17        14.04        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6805 
      119.93        35.97       117.07        31.96        11.11        34.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6303 TCGA-G4-6306 
       43.04        33.67        13.25         8.35        65.85        44.68 
TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 
       55.04        39.42        61.91        36.00        26.43        46.75 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 
       10.98        19.33         9.93        15.65        12.79        16.80 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL 
       42.77        29.46        32.98         8.42        21.90        38.70 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       60.13        11.90        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        24.36        20.02 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       86.63        65.98        11.84        36.03        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        7.07        36.03        24.00         1.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       34.03         2.01        50.04         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       19.04         1.02        17.95        35.01         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-4021 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
        3.98        13.94         6.02        23.01        37.02         1.02 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        41.00        38.04        38.56        43.20        27.55 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5918 
       26.43         6.05        33.17        13.78        44.78         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       21.01        25.05        13.97        31.00        10.98        44.02 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 
      129.27        24.13        51.48         3.48         4.18        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-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 
       28.57         0.39        19.66        37.18        11.87        12.46 

$`DEL PEAK 38(17P12) WILD-TYPE`
TCGA-A6-2682 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.94        58.03        13.02         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 
        0.99        17.95         0.92        19.04        19.04        14.93 
TCGA-AA-3860 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6895 
       31.07        12.99        24.00        19.07        39.06        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6321 TCGA-G4-6586 
       10.88        75.95       100.01        28.21        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-A015 
       26.17        79.69        10.39         8.02        19.99        36.03 
TCGA-G5-6233 TCGA-G5-6641 TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 
       18.28        26.43        12.66         9.53        46.65        42.90 
TCGA-A6-2679 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-5661 TCGA-A6-5662 
       44.91        37.02        32.75        36.53        33.53        23.61 
TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-6653 
       22.09        22.06         8.38        25.08        21.76        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        56.25         9.63 
TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
        3.02        35.01        63.98         1.02        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3538 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3664 
       29.00        26.01        29.95        20.98         6.97        54.02 
TCGA-AA-3675 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       47.05        15.02        11.01         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3846 
        0.99         1.02        17.98        15.95         0.00        17.03 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3947 
        0.00         0.00        36.03        53.00        31.00        33.01 
TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3973 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 
       26.01         2.01        13.05        25.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       38.04        30.02        18.05        18.05         4.01         0.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R 
       34.98        15.02        31.00        38.07         1.02        35.01 
TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
        1.02        26.01        51.98         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-6197 
       18.05        12.16        83.24         0.92        27.09        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4615 
       17.82        17.26        19.33        18.84        58.39        32.94 
TCGA-AZ-5403 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 
       62.79        49.41         6.77        11.74        12.36        12.39 
TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       12.76        10.06        17.56        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 
       37.02        26.04        22.98        30.08        32.02        15.02 
TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6168 TCGA-CM-6171 
       15.02        12.00        14.04        16.04        12.99        14.04 
TCGA-CM-6674 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6680 TCGA-D5-6529 TCGA-D5-6530 
       12.95        11.08        11.01        12.03        20.19        20.42 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 
       17.85         4.80        16.14        12.39         9.44        11.64 
TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1D6 TCGA-DM-A1DA 
       13.35        12.00        10.26       119.70        49.91         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-DM-A28M 
      135.65         7.76        81.37        60.79        98.24        95.18 
TCGA-F4-6459 TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
        8.61        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6806 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 
       41.42         0.53        47.41        35.31       133.18        82.39 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6309 TCGA-G4-6322 TCGA-G4-6323 
       74.56        67.30        53.62        85.48        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A5IV TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2687 
       74.79        18.18        19.33        31.30        70.03        46.92 
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3583 TCGA-AG-3592 TCGA-AG-3599 TCGA-AG-3600 
       16.83        24.59        20.05        34.03        12.03         6.05 
TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       29.98         0.99        19.99        36.95        13.02        14.01 
TCGA-AG-3901 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 
       25.02        46.03        20.98         9.07         1.02        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6623 TCGA-CI-6624 
       38.96        61.97         2.50        19.46        47.44        48.20 
TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6681 
       78.12        26.04        31.00        12.00        51.98        25.97 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 TCGA-EI-6883 
       32.61        20.55        19.96        15.85         8.61        11.51 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6572 
       13.64        17.46        32.19        36.49        38.14        47.08 

  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                         0.2                          0.0 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                      148.01                       135.65 
  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE 
                       22.47                        21.06 
[1] "0.2 - 148.0 (22.5)" "0.0 - 135.7 (21.1)"
[1] "hr=" "1.1"
D62V2, continuous
D62V3, binary
                              cls
clus                             0   1
  DEL PEAK 38(17P12) MUTATED   251 113
  DEL PEAK 38(17P12) WILD-TYPE 197  49
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED    251  113
  DEL PEAK 38(17P12) WILD-TYPE  197   49
        clus
vv       DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  COLON                         251                          197
  RECTUM                        113                           49
[1] 2 2
[1] FALSE
                              vv
clus                           STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 38(17P12) MUTATED        53        0       20        87         4
  DEL PEAK 38(17P12) WILD-TYPE      51        1       17        85         8
                              vv
clus                           STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 38(17P12) MUTATED           1        15         12         54
  DEL PEAK 38(17P12) WILD-TYPE         1         9          3         30
                              vv
clus                           STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 38(17P12) MUTATED           42       46        18         2
  DEL PEAK 38(17P12) WILD-TYPE         13       17         6         0
D62V4, multiclass
            clus
vv           DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  STAGE I                            53                           51
  STAGE IA                            0                            1
  STAGE II                           20                           17
  STAGE IIA                          87                           85
  STAGE IIB                           4                            8
  STAGE IIC                           1                            1
  STAGE III                          15                            9
  STAGE IIIA                         12                            3
  STAGE IIIB                         54                           30
  STAGE IIIC                         42                           13
  STAGE IV                           46                           17
  STAGE IVA                          18                            6
  STAGE IVB                           2                            0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  DEL PEAK 38(17P12) MUTATED     9  59 256  43
  DEL PEAK 38(17P12) WILD-TYPE  11  46 161  26
D62V5, multiclass
    clus
vv   DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  T1                          9                           11
  T2                         59                           46
  T3                        256                          161
  T4                         43                           26
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            N0  N1  N2
  DEL PEAK 38(17P12) MUTATED   180 103  83
  DEL PEAK 38(17P12) WILD-TYPE 166  47  32
D62V6, multiclass
    clus
vv   DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  N0                        180                          166
  N1                        103                           47
  N2                         83                           32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                              cls
clus                             0   1
  DEL PEAK 38(17P12) MUTATED   261  66
  DEL PEAK 38(17P12) WILD-TYPE 192  22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED    261   66
  DEL PEAK 38(17P12) WILD-TYPE  192   22
   clus
vv  DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  0                        261                          192
  1                         66                           22
[1] 2 2
[1] FALSE
D62V8, binary
                              cls
clus                             0   1
  DEL PEAK 38(17P12) MUTATED   168 200
  DEL PEAK 38(17P12) WILD-TYPE 121 125
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED    168  200
  DEL PEAK 38(17P12) WILD-TYPE  121  125
        clus
vv       DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  FEMALE                        168                          121
  MALE                          200                          125
[1] 2 2
[1] FALSE
D62V9, binary
                              cls
clus                             0   1
  DEL PEAK 38(17P12) MUTATED   287  18
  DEL PEAK 38(17P12) WILD-TYPE 195  11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED    287   18
  DEL PEAK 38(17P12) WILD-TYPE  195   11
     clus
vv    DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  NO                         287                          195
  YES                         18                           11
[1] 2 2
[1] FALSE
                              vv
clus                           COLON ADENOCARCINOMA
  DEL PEAK 38(17P12) MUTATED                    232
  DEL PEAK 38(17P12) WILD-TYPE                  150
                              vv
clus                           COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(17P12) MUTATED                              16
  DEL PEAK 38(17P12) WILD-TYPE                            46
                              vv
clus                           RECTAL ADENOCARCINOMA
  DEL PEAK 38(17P12) MUTATED                     105
  DEL PEAK 38(17P12) WILD-TYPE                    41
                              vv
clus                           RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 38(17P12) MUTATED                                6
  DEL PEAK 38(17P12) WILD-TYPE                              7
D62V10, multiclass
                                clus
vv                               DEL PEAK 38(17P12) MUTATED
  COLON ADENOCARCINOMA                                  232
  COLON MUCINOUS ADENOCARCINOMA                          16
  RECTAL ADENOCARCINOMA                                 105
  RECTAL MUCINOUS ADENOCARCINOMA                          6
                                clus
vv                               DEL PEAK 38(17P12) WILD-TYPE
  COLON ADENOCARCINOMA                                    150
  COLON MUCINOUS ADENOCARCINOMA                            46
  RECTAL ADENOCARCINOMA                                    41
  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"
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 38(17P12) MUTATED   262   4  26  13
  DEL PEAK 38(17P12) WILD-TYPE 184   2  11  16
D62V11, multiclass
    clus
vv   DEL PEAK 38(17P12) MUTATED DEL PEAK 38(17P12) WILD-TYPE
  R0                        262                          184
  R1                          4                            2
  R2                         26                           11
  RX                         13                           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"
D62V12, continuous
D62V13, binary
                              cls
clus                             0   1
  DEL PEAK 38(17P12) MUTATED     4 207
  DEL PEAK 38(17P12) WILD-TYPE   1 145
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 38(17P12) MUTATED      4  207
  DEL PEAK 38(17P12) WILD-TYPE    1  145
                        clus
vv                       DEL PEAK 38(17P12) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        207
                        clus
vv                       DEL PEAK 38(17P12) WILD-TYPE
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          145
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 39(17Q24.3) MUTATION ANALYSIS
D63V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 39(17Q24.3) MUTATED    68  25
  DEL PEAK 39(17Q24.3) WILD-TYPE 398 103
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                            93                            501 
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                            25                            103 
$`DEL PEAK 39(17Q24.3) MUTATED`
TCGA-A6-6649 TCGA-AA-3520 TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3976 
       24.16        24.03        19.99         6.05        19.00        26.01 
TCGA-CK-5912 TCGA-AG-3611 TCGA-AG-A00H TCGA-BM-6198 TCGA-A6-2671 TCGA-A6-2674 
       49.08        13.94        25.97        21.24        43.76        43.76 
TCGA-A6-2684 TCGA-A6-4107 TCGA-A6-5657 TCGA-A6-6138 TCGA-A6-6648 TCGA-AA-3542 
       37.05        32.45        31.63        22.52        25.18        12.99 
TCGA-AA-3549 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3842 
       21.01         2.01        50.04        37.05        10.06        37.02 
TCGA-AA-3858 TCGA-AA-3869 TCGA-AA-3941 TCGA-AA-3989 TCGA-AA-A00F TCGA-AA-A00Q 
       31.07        27.02        24.00         7.96        34.03        42.02 
TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01T TCGA-AA-A02E TCGA-AA-A02F TCGA-AD-6899 
       10.98        32.02        33.04         2.96        39.98         5.79 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-6196 TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-6600 
       22.42        26.47         0.20        17.85        18.84        12.10 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CM-4747 TCGA-CM-4751 TCGA-CM-5862 TCGA-CM-5864 
       12.59        12.20        25.02        27.02         5.03        15.02 
TCGA-CM-6170 TCGA-D5-5537 TCGA-D5-6534 TCGA-D5-6539 TCGA-D5-6929 TCGA-D5-6932 
       15.02        45.40        43.27        12.49        13.41        11.38 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A280 
       38.20       130.65        12.59       140.38        44.32         7.76 
TCGA-DM-A28H TCGA-F4-6460 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6809 TCGA-G4-6295 
      117.07        31.96        35.74         1.55        13.25         8.35 
TCGA-NH-A50U TCGA-NH-A6GA TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QL-A97D TCGA-AF-4110 
       10.98         9.93        12.79        42.77        21.90        29.98 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3591 
       24.36        65.98         7.07        36.03         1.02        34.03 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-A008 TCGA-AG-A016 TCGA-AG-A02X 
        1.02        32.02        28.04        13.94         9.07        41.00 
TCGA-AH-6643 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DF 
       43.20        13.97        31.00        10.98        12.62        24.13 
TCGA-EI-6508 TCGA-EI-6881 TCGA-F5-6814 
       20.91        16.41        37.18 

$`DEL PEAK 39(17Q24.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        14.53         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 
       13.02        37.05        36.03         8.05        19.07        34.03 
TCGA-AA-3543 TCGA-AA-3552 TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3672 
        0.99        13.02        17.95        23.01        19.99         0.92 
TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 
       36.00        85.05        19.04        19.04        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       24.03        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 
       24.00        19.07        38.04        21.99        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 
       15.52        25.08        10.88        75.95       106.75       100.01 
TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6314 
        1.94         5.88        28.21        23.51        63.62        35.93 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 
       22.09        35.80        26.17        91.79        79.69        17.85 
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        19.99        17.03        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       36.03        31.00        51.98        18.28        55.76        26.43 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE 
       15.62         4.80        12.66         1.61         9.53        39.45 
TCGA-A6-2672 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 
       46.65        43.43        42.90        42.28        44.91        35.11 
TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       16.57        37.25        37.02        34.65        32.75        36.53 
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-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 
       22.06        32.71        29.16        27.09        24.13         8.38 
TCGA-A6-6142 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6654 
       25.08        20.61        21.76        24.69        24.39        23.87 
TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A567 
       20.12        19.66        20.28        16.24        24.92        61.84 
TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       56.25         9.63         5.03         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 TCGA-AA-3514 TCGA-AA-3517 
       37.05        35.01        63.98         6.97         1.02        38.99 
TCGA-AA-3518 TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         9.07        19.07         0.00        29.00        29.00 
TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 
       26.01        14.01        33.99        24.00        29.95        20.98 
TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 
       13.94        61.02        78.08         6.97        54.02        14.01 
TCGA-AA-3675 TCGA-AA-3678 TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 
       47.05        47.01        15.02        11.01         5.98         5.03 
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-3841 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 
       15.95        38.99        36.95         0.00        17.03        10.06 
TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3856 
        0.00        33.07         0.00        36.03        32.05         0.99 
TCGA-AA-3864 TCGA-AA-3866 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       53.00        17.03        18.05        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3971 
       26.01        20.98        34.03         2.01        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A004 
       13.05        34.06        25.02        27.02        27.02        13.94 
TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N 
       38.04        19.00        30.02        18.05        18.05         4.01 
TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 
       27.02         0.99        17.03        14.99        34.98        15.02 
TCGA-AA-A01C TCGA-AA-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-A01Z TCGA-AA-A029 
       35.01         1.02         1.02        26.01        37.02        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-6889 TCGA-AD-6890 TCGA-AD-6963 
       18.05        40.96        12.16        83.24        24.53        27.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         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-AY-A71X 
        0.95        33.01        21.44        17.82        17.26        19.33 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4616 
      109.28        58.39         1.41         5.65        32.94         5.13 
TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
       22.36        65.00        62.79        88.21        49.41         6.77 
TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 
       29.56         5.23        11.74         3.19        12.69        12.36 
TCGA-CA-5256 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.46        12.39        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5914 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 
       21.99        21.14        82.95         2.01       124.27        23.05 
TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4750 TCGA-CM-4752 TCGA-CM-5341 
       20.02        37.02        26.04         8.02        13.02        29.06 
TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5863 
       22.03        22.98        30.08        32.02        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-6171 TCGA-CM-6172 
       21.99        14.99        12.99        13.02        14.04        11.01 
TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       12.95        13.05        11.08        11.08        11.01        10.06 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 
       12.03        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 
       20.42        17.75        18.25        25.48        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6920 
        4.80        17.13        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-A0X9 TCGA-DM-A0XD TCGA-DM-A1D4 
       13.35        12.00        10.26       119.70        24.43        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB TCGA-DM-A282 
       49.91        13.32         7.50       131.51       135.65       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-A28K TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6570 
       98.24        95.18         8.61        11.11        35.74         6.18 
TCGA-F4-6703 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
       47.87        34.42        41.42        43.04        33.67         0.53 
TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 
       47.41        35.31       133.18        82.39        74.56        67.30 
TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 
       65.85        53.62        44.68        55.04        85.48        39.42 
TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 
       61.91        36.00        26.43        26.04        13.78        46.75 
TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A8F8 
       74.79        18.18        19.33        19.33        15.65        16.80 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-RU-A8FL TCGA-SS-A7HO 
       29.46        32.98         8.42        31.30        38.70        60.13 
TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       11.90        70.03        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 
       13.55        37.97        34.49        37.74        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       24.59        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00        46.03        34.03        34.03         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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       36.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       19.99        36.03        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 
       20.98         6.02        23.01        37.02         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        38.96        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        2.50        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
       21.01        25.05        26.04        31.00        12.00        51.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31         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        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       28.57         0.39        32.19        36.49        19.66        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE 
                         24.00                          21.99 
[1] "0.2 - 140.4 (24.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.5"
D63V2, continuous
D63V3, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q24.3) MUTATED    69  25
  DEL PEAK 39(17Q24.3) WILD-TYPE 379 137
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q24.3) MUTATED     69   25
  DEL PEAK 39(17Q24.3) WILD-TYPE  379  137
        clus
vv       DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  COLON                            69                            379
  RECTUM                           25                            137
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 39(17Q24.3) MUTATED        15        0        5        15         0
  DEL PEAK 39(17Q24.3) WILD-TYPE      89        1       32       157        12
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 39(17Q24.3) MUTATED           0         4          4         11
  DEL PEAK 39(17Q24.3) WILD-TYPE         2        20         11         73
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 39(17Q24.3) MUTATED           16       12         9         1
  DEL PEAK 39(17Q24.3) WILD-TYPE         39       51        15         1
D63V4, multiclass
            clus
vv           DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  STAGE I                              15                             89
  STAGE IA                              0                              1
  STAGE II                              5                             32
  STAGE IIA                            15                            157
  STAGE IIB                             0                             12
  STAGE IIC                             0                              2
  STAGE III                             4                             20
  STAGE IIIA                            4                             11
  STAGE IIIB                           11                             73
  STAGE IIIC                           16                             39
  STAGE IV                             12                             51
  STAGE IVA                             9                             15
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 39(17Q24.3) MUTATED     0  18  63  14
  DEL PEAK 39(17Q24.3) WILD-TYPE  20  87 354  55
D63V5, multiclass
    clus
vv   DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  T1                            0                             20
  T2                           18                             87
  T3                           63                            354
  T4                           14                             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
  DEL PEAK 39(17Q24.3) MUTATED    38  30  27
  DEL PEAK 39(17Q24.3) WILD-TYPE 308 120  88
D63V6, multiclass
    clus
vv   DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  N0                           38                            308
  N1                           30                            120
  N2                           27                             88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q24.3) MUTATED    60  21
  DEL PEAK 39(17Q24.3) WILD-TYPE 393  67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q24.3) MUTATED     60   21
  DEL PEAK 39(17Q24.3) WILD-TYPE  393   67
   clus
vv  DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  0                           60                            393
  1                           21                             67
[1] 2 2
[1] FALSE
D63V8, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q24.3) MUTATED    39  56
  DEL PEAK 39(17Q24.3) WILD-TYPE 250 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q24.3) MUTATED     39   56
  DEL PEAK 39(17Q24.3) WILD-TYPE  250  269
        clus
vv       DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  FEMALE                           39                            250
  MALE                             56                            269
[1] 2 2
[1] FALSE
D63V9, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q24.3) MUTATED    73   5
  DEL PEAK 39(17Q24.3) WILD-TYPE 409  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q24.3) MUTATED     73    5
  DEL PEAK 39(17Q24.3) WILD-TYPE  409   24
     clus
vv    DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  NO                            73                            409
  YES                            5                             24
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 39(17Q24.3) MUTATED                     59
  DEL PEAK 39(17Q24.3) WILD-TYPE                  323
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(17Q24.3) MUTATED                               9
  DEL PEAK 39(17Q24.3) WILD-TYPE                            53
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 39(17Q24.3) MUTATED                      22
  DEL PEAK 39(17Q24.3) WILD-TYPE                   124
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 39(17Q24.3) MUTATED                                2
  DEL PEAK 39(17Q24.3) WILD-TYPE                             11
D63V10, multiclass
                                clus
vv                               DEL PEAK 39(17Q24.3) MUTATED
  COLON ADENOCARCINOMA                                     59
  COLON MUCINOUS ADENOCARCINOMA                             9
  RECTAL ADENOCARCINOMA                                    22
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 39(17Q24.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      323
  COLON MUCINOUS ADENOCARCINOMA                              53
  RECTAL ADENOCARCINOMA                                     124
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 39(17Q24.3) MUTATED    63   1   8   6
  DEL PEAK 39(17Q24.3) WILD-TYPE 383   5  29  23
D63V11, multiclass
    clus
vv   DEL PEAK 39(17Q24.3) MUTATED DEL PEAK 39(17Q24.3) WILD-TYPE
  R0                           63                            383
  R1                            1                              5
  R2                            8                             29
  RX                            6                             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"
D63V12, continuous
D63V13, binary
                                cls
clus                               0   1
  DEL PEAK 39(17Q24.3) MUTATED     0  54
  DEL PEAK 39(17Q24.3) WILD-TYPE   5 298
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 39(17Q24.3) MUTATED      0   54
  DEL PEAK 39(17Q24.3) WILD-TYPE    5  298
                        clus
vv                       DEL PEAK 39(17Q24.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           54
                        clus
vv                       DEL PEAK 39(17Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            298
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 40(18P11.31) MUTATION ANALYSIS
D64V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 40(18P11.31) MUTATED   285  72
  DEL PEAK 40(18P11.31) WILD-TYPE 181  56
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                            357                             237 
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                             72                              56 
$`DEL PEAK 40(18P11.31) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3522 
       24.33        45.60        13.94        14.53         1.02        37.05 
TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 
       19.07        34.03        13.02        23.01        19.99        19.99 
TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 TCGA-AA-3844 TCGA-AA-3860 
        6.05        19.00        36.00        85.05        14.93        31.07 
TCGA-AA-3867 TCGA-AA-3939 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00L 
       24.03        12.99        50.99        26.01        24.00        38.04 
TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-G4-6294 
       21.99        15.52       106.75         1.94        49.08        28.21 
TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 
       23.51        63.62        91.79        17.85        10.39        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N 
       19.99        17.03        17.03        25.97        15.95        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T 
       51.98        21.24        18.28        55.76        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       12.66         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5659 TCGA-A6-5660 
       34.65        36.53        32.45        32.91        30.44        29.19 
TCGA-A6-5662 TCGA-A6-5664 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 
       23.61        22.09        32.71        29.16        27.09        24.13 
TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6652 TCGA-A6-6654 
       25.08        25.18        20.61        21.76        24.69        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       20.28        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3526 
        1.02        37.05         6.97        38.99         9.07        19.07 
TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3553 TCGA-AA-3561 
       29.00        26.01        14.01        33.99        24.00        13.94 
TCGA-AA-3660 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       78.08         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       37.05        25.02        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 TCGA-AA-3869 
       10.06        33.07         0.99        31.07        17.03        27.02 
TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 
       18.05        24.00        20.98        34.03        21.99        16.08 
TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F 
       13.05        34.06         7.96        13.94        19.00        34.03 
TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       27.02        42.02        14.99        15.02        15.02        32.02 
TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A02E TCGA-AA-A02F 
       31.00         1.02        33.04        26.01         2.96        39.98 
TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 
        2.01         5.03        41.00        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4071 
       22.42        27.42        26.47        16.44        14.50         0.95 
TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4614 
       33.01        17.26        17.85        18.84       109.28         5.65 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-6600 TCGA-AZ-6603 
        5.13        22.36        65.00        62.79        12.10        29.56 
TCGA-AZ-6605 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 
        5.23        12.69        12.46        12.59        12.59        12.20 
TCGA-CA-6719 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4752 
       14.30        21.99         2.01        25.02         8.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       29.06        22.03        30.08         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
       14.04        29.03        16.04        21.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 TCGA-D5-5537 
       11.01        11.08        11.01        10.06        12.03        45.40 
TCGA-D5-5538 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6532 TCGA-D5-6533 
       54.61        56.09        55.92        20.19        18.25        25.48 
TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6898 TCGA-D5-6923 TCGA-D5-6924 
       17.85        17.13        12.49         7.53        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04        13.41        11.38        24.43        38.20       130.65 
TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A282 TCGA-DM-A28A 
       13.32        12.59       140.38        44.32       139.17        26.47 
TCGA-DM-A28E TCGA-DM-A28F TCGA-DM-A28H TCGA-DM-A28M TCGA-F4-6460 TCGA-F4-6461 
      119.93        35.97       117.07        95.18        31.96        11.11 
TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 
       35.74         1.55        34.42        41.42        43.04        33.67 
TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6303 
       13.25         0.53        47.41         8.35        82.39        65.85 
TCGA-G4-6307 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T 
       55.04        61.91        36.00        46.75        74.79        18.18 
TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       10.98        19.33        12.79        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 
        8.42        21.90        38.70        60.13        11.90        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 
       39.48        17.23        43.04        13.55        34.49        37.74 
TCGA-AF-4110 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       29.98        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3592 
        7.07        36.03        20.05        24.00        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       34.03        50.04         0.99        15.95        20.98         7.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       29.98        37.02        32.98         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       36.95        35.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       19.99        28.04        36.03         1.02         3.98        46.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        37.02         9.07         1.02         1.02 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        41.00        38.04        38.56        43.20        27.55 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       26.43         6.05        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        51.48         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.55        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-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
       19.66        11.87        12.46 

$`DEL PEAK 40(18P11.31) WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 
       24.16        58.03        13.02        24.03        36.03         8.05 
TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 
        0.99        17.95         0.92        19.04        19.04        29.98 
TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 
       24.00         2.01        19.07        39.06        21.37        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-DM-A285 TCGA-G4-6314 TCGA-G4-6321 
       10.88        75.95       100.01         5.88        35.93        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-A015 TCGA-G5-6641 
       35.80        26.17        79.69         8.02        36.03        26.43 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-2686 TCGA-A6-3809 TCGA-A6-5657 
        9.53        46.65        42.90        37.02        32.75        31.63 
TCGA-A6-5661 TCGA-A6-5665 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6653 TCGA-A6-6780 
       33.53        22.06        22.52         8.38        24.39        20.12 
TCGA-A6-6781 TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 
       19.66        16.24        24.92         3.02        35.01        63.98 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3549 
        1.02         1.02         0.00        29.00        12.99        21.01 
TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3675 
       29.95        20.98        61.02         6.97        54.02        47.05 
TCGA-AA-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
       11.01         5.98         5.03        26.99        10.06        35.05 
TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 
        0.99         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 
        0.00        36.03        32.05        53.00        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 
       33.01        26.01         2.01        25.02        27.02        27.02 
TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R 
       38.04        30.02        18.05        18.05         4.01         0.99 
TCGA-AA-A00U TCGA-AA-A010 TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P 
       17.03        34.98        10.98        12.00        31.00        38.07 
TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-A029 TCGA-AA-A02O 
        1.02        35.01         1.02        37.02        51.98         0.92 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5820 
       22.03        39.98        18.05        12.16        83.24         0.46 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4070 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 
        0.92        27.09        16.31         0.20        21.44        17.82 
TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-5407 TCGA-AZ-6598 
       19.33        58.39         1.41        32.94        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6717 
        6.77        11.74         3.19        12.36        12.39        12.76 
TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 
       10.06        17.56       148.01        85.45        70.16        15.62 
TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 
       51.32        21.14        82.95       124.27        23.05        20.02 
TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-4751 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       37.02        26.04        27.02        22.98        32.02        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-CM-6675 TCGA-CM-6676 TCGA-D5-5539 TCGA-D5-6530 TCGA-D5-6531 
       12.95        13.05        11.08        19.59        20.42        17.75 
TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 
       43.27        15.12         4.80        16.14        15.58        12.39 
TCGA-D5-6922 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 
       10.13         9.44        11.64        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A1HB 
      119.70        92.75        49.91         7.50       131.51       135.65 
TCGA-DM-A280 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28G TCGA-DM-A28K TCGA-F4-6459 
        7.76        14.04        81.37        60.79        98.24         8.61 
TCGA-F4-6463 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 
       35.74         6.18        47.87        35.31       133.18        74.56 
TCGA-G4-6302 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6320 
       67.30        53.62        44.68        85.48        39.42        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-QG-A5YW 
       26.04        13.78        19.33         9.93        15.65        29.46 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       31.30        70.03        37.97        16.83        24.36        24.59 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3599 
       12.00        32.02         1.02        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 
        6.05        19.99         0.99         0.99        19.04        17.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A00Y TCGA-AG-A025 
       13.02        14.01        14.04        20.98        23.01        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 
       38.96        61.97         2.50        19.46        12.62        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 
       37.18        38.14        47.08 

  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                           0.39                            0.00 
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                         140.38                          148.01 
  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE 
                          24.00                           20.12 
[1] "0.4 - 140.4 (24.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.2"
D64V2, continuous
D64V3, binary
                                 cls
clus                                0   1
  DEL PEAK 40(18P11.31) MUTATED   244 122
  DEL PEAK 40(18P11.31) WILD-TYPE 204  40
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.31) MUTATED    244  122
  DEL PEAK 40(18P11.31) WILD-TYPE  204   40
        clus
vv       DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  COLON                            244                             204
  RECTUM                           122                              40
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 40(18P11.31) MUTATED        57        0       15        97         5
  DEL PEAK 40(18P11.31) WILD-TYPE      47        1       22        75         7
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 40(18P11.31) MUTATED           2        10         10         54
  DEL PEAK 40(18P11.31) WILD-TYPE         0        14          5         30
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 40(18P11.31) MUTATED           34       48        23         1
  DEL PEAK 40(18P11.31) WILD-TYPE         21       15         1         1
D64V4, multiclass
            clus
vv           DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  STAGE I                               57                              47
  STAGE IA                               0                               1
  STAGE II                              15                              22
  STAGE IIA                             97                              75
  STAGE IIB                              5                               7
  STAGE IIC                              2                               0
  STAGE III                             10                              14
  STAGE IIIA                            10                               5
  STAGE IIIB                            54                              30
  STAGE IIIC                            34                              21
  STAGE IV                              48                              15
  STAGE IVA                             23                               1
  STAGE IVB                              1                               1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 40(18P11.31) MUTATED    11  61 254  42
  DEL PEAK 40(18P11.31) WILD-TYPE   9  44 163  27
D64V5, multiclass
    clus
vv   DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  T1                            11                               9
  T2                            61                              44
  T3                           254                             163
  T4                            42                              27
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               N0  N1  N2
  DEL PEAK 40(18P11.31) MUTATED   190 104  73
  DEL PEAK 40(18P11.31) WILD-TYPE 156  46  42
D64V6, multiclass
    clus
vv   DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  N0                           190                             156
  N1                           104                              46
  N2                            73                              42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                                 cls
clus                                0   1
  DEL PEAK 40(18P11.31) MUTATED   257  72
  DEL PEAK 40(18P11.31) WILD-TYPE 196  16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.31) MUTATED    257   72
  DEL PEAK 40(18P11.31) WILD-TYPE  196   16
   clus
vv  DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  0                           257                             196
  1                            72                              16
[1] 2 2
[1] FALSE
D64V8, binary
                                 cls
clus                                0   1
  DEL PEAK 40(18P11.31) MUTATED   170 199
  DEL PEAK 40(18P11.31) WILD-TYPE 119 126
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.31) MUTATED    170  199
  DEL PEAK 40(18P11.31) WILD-TYPE  119  126
        clus
vv       DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  FEMALE                           170                             119
  MALE                             199                             126
[1] 2 2
[1] FALSE
D64V9, binary
                                 cls
clus                                0   1
  DEL PEAK 40(18P11.31) MUTATED   295  18
  DEL PEAK 40(18P11.31) WILD-TYPE 187  11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.31) MUTATED    295   18
  DEL PEAK 40(18P11.31) WILD-TYPE  187   11
     clus
vv    DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  NO                            295                             187
  YES                            18                              11
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 40(18P11.31) MUTATED                    232
  DEL PEAK 40(18P11.31) WILD-TYPE                  150
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 40(18P11.31) MUTATED                               9
  DEL PEAK 40(18P11.31) WILD-TYPE                            53
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 40(18P11.31) MUTATED                     116
  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
D64V10, multiclass
                                clus
vv                               DEL PEAK 40(18P11.31) MUTATED
  COLON ADENOCARCINOMA                                     232
  COLON MUCINOUS ADENOCARCINOMA                              9
  RECTAL ADENOCARCINOMA                                    116
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 40(18P11.31) WILD-TYPE
  COLON ADENOCARCINOMA                                       150
  COLON MUCINOUS ADENOCARCINOMA                               53
  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"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 40(18P11.31) MUTATED   264   3  29  14
  DEL PEAK 40(18P11.31) WILD-TYPE 182   3   8  15
D64V11, multiclass
    clus
vv   DEL PEAK 40(18P11.31) MUTATED DEL PEAK 40(18P11.31) WILD-TYPE
  R0                           264                             182
  R1                             3                               3
  R2                            29                               8
  RX                            14                              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"
D64V12, continuous
D64V13, binary
                                 cls
clus                                0   1
  DEL PEAK 40(18P11.31) MUTATED     4 214
  DEL PEAK 40(18P11.31) WILD-TYPE   1 138
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 40(18P11.31) MUTATED      4  214
  DEL PEAK 40(18P11.31) WILD-TYPE    1  138
                        clus
vv                       DEL PEAK 40(18P11.31) MUTATED
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           214
                        clus
vv                       DEL PEAK 40(18P11.31) WILD-TYPE
  HISPANIC OR LATINO                                   1
  NOT HISPANIC OR LATINO                             138
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 41(18Q12.2) MUTATION ANALYSIS
D65V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 41(18Q12.2) MUTATED   318  83
  DEL PEAK 41(18Q12.2) WILD-TYPE 148  45
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                           401                            193 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                            83                             45 
$`DEL PEAK 41(18Q12.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        13.94        14.53         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       37.05        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6888 TCGA-AD-6964 
       50.99        26.01        24.00        21.99        15.52        10.88 
TCGA-AZ-4681 TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 
      106.75         1.94        49.08         5.88        28.21        23.51 
TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 
       63.62        35.93        91.79        17.85        10.39        13.94 
TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N 
       19.99        17.03        17.03        25.97        15.95        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B 
       51.98        21.24        18.28        55.76        26.43        15.62 
TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 
        4.80        12.66         1.61        39.45        43.76        43.76 
TCGA-A6-2675 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 
       43.43        42.28        44.91        35.11        16.57        37.05 
TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 
       37.25        37.02        34.65        36.53        32.45        32.91 
TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 
       31.63        30.44        29.19        23.61        32.71        29.16 
TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       27.09        22.52        24.13        25.18        20.61        21.76 
TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 
       23.87        20.28        61.84        56.25         9.63         5.03 
TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 
        7.04         1.02        37.05         6.97        38.99         9.07 
TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 TCGA-AA-3548 
       19.07        29.00        26.01        12.99        14.01        33.99 
TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3666 
       21.01        24.00        13.94        61.02        78.08         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-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 TCGA-AA-3848 
       25.02        38.99        36.95        37.02        17.03        10.06 
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-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       24.00        20.98        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00K 
       34.06        27.02         7.96        19.00        34.03        18.05 
TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D 
       42.02        17.03        14.99        15.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z 
       32.02        31.00         1.02        33.04        26.01        37.02 
TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W 
        2.96        39.98         2.01         5.03         0.92        41.00 
TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 
       40.96        24.53         5.79        22.42        27.42        26.47 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L 
       16.44         0.46        14.50        16.31        33.01        17.26 
TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 
       17.85        18.84       109.28         5.13        22.36        65.00 
TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-CA-5254 
       62.79        88.21        12.10        29.56         5.23        12.69 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
       12.46        12.59        12.59        12.20        14.30       148.01 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       21.99         2.01        25.02         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       29.06        22.03        30.08         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
       14.04        29.03        16.04        21.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-CM-6680 
       11.01        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 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6541 
       18.25        25.48        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-A288 TCGA-DM-A28A TCGA-DM-A28E TCGA-DM-A28H TCGA-DM-A28M 
      139.17        14.04        26.47       119.93       117.07        95.18 
TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 
        8.61        31.96        11.11        35.74         1.55        34.42 
TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 
       41.42        43.04        13.25         0.53        47.41         8.35 
TCGA-G4-6297 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 
       82.39        65.85        44.68        55.04        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       36.00        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QL-A97D 
       12.79        16.80        42.77        32.98         8.42        21.90 
TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       38.70        60.13        11.90        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
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        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
       24.00        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 
       50.04         6.05         0.99        15.95        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        0.99        29.98        37.02        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 
       19.99         1.02        17.95        36.95        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02         3.98        46.03        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       23.01        37.02         1.02         1.02         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04        38.56        43.20        27.55        26.43 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05       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         3.48         4.18        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        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        11.87        12.46        47.08 

$`DEL PEAK 41(18Q12.2) WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       24.16        58.03        13.02         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00L 
        0.92        19.04        19.04        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-G4-6321 
       39.06        21.37        25.08        75.95       100.01        22.09 
TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-A015 TCGA-5M-AAT6 
       35.80        26.17        79.69         8.02        36.03         9.53 
TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 
       46.65        42.90        32.75        33.53        22.09        22.06 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6653 TCGA-A6-6780 TCGA-A6-6781 
        8.38        25.08        24.69        24.39        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 
       16.24        24.92         3.02        35.01        63.98         1.02 
TCGA-AA-3518 TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 
        1.02         0.00        29.00        29.95        20.98         6.97 
TCGA-AA-3664 TCGA-AA-3675 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 
       54.02        47.05        11.01         5.03        26.99        10.06 
TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 
       35.05         0.99         1.02        17.98        15.95         0.00 
TCGA-AA-3850 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3864 TCGA-AA-3877 
        0.00         0.00        36.03        32.05        53.00        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3994 
        2.01        33.01        26.01         2.01        25.02        27.02 
TCGA-AA-A004 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O 
       13.94        38.04        30.02        18.05         4.01        27.02 
TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
        0.99        34.98        12.00        31.00        38.07         1.02 
TCGA-AA-A01R TCGA-AA-A01V TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F 
       35.01         1.02        51.98        22.03        39.98        18.05 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 
       12.16        83.24         0.92        27.09         0.95         0.20 
TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 
       21.44        17.82        19.33        58.39         1.41         5.65 
TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5255 
       32.94        49.41         6.77        11.74         3.19        12.36 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.39        12.76        10.06        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14        82.95       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        32.02        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-CM-6675 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6534 TCGA-D5-6535 
       12.95        13.05        20.42        17.75        43.27        15.12 
TCGA-D5-6537 TCGA-D5-6540 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 
        4.80        16.14        12.39         9.44        11.64        13.35 
TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A28C 
       12.00        10.26       119.70       135.65         7.76        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        35.74         6.18        47.87 
TCGA-F4-6808 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6304 
       33.67        35.31       133.18        74.56        67.30        53.62 
TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GA 
       85.48        26.43        26.04        13.78        19.33         9.93 
TCGA-NH-A6GB TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 TCGA-AG-3586 
       15.65        29.46        31.30        70.03        16.83         1.02 
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-A016 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 
        9.07        49.97        61.97         2.50        19.46        12.62 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 
       32.61        19.96         8.61        17.46         9.96        37.18 
TCGA-F5-6861 
       38.14 

  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                          0.39                           0.00 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                        148.01                         135.65 
  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE 
                         23.51                          20.12 
[1] "0.4 - 148.0 (23.5)" "0.0 - 135.7 (20.1)"
[1] "hr=" "1.1"
D65V2, continuous
D65V3, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q12.2) MUTATED   272 139
  DEL PEAK 41(18Q12.2) WILD-TYPE 176  23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED    272  139
  DEL PEAK 41(18Q12.2) WILD-TYPE  176   23
        clus
vv       DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  COLON                           272                            176
  RECTUM                          139                             23
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 41(18Q12.2) MUTATED        60        0       22       105         5
  DEL PEAK 41(18Q12.2) WILD-TYPE      44        1       15        67         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 41(18Q12.2) MUTATED           2        14         13         61
  DEL PEAK 41(18Q12.2) WILD-TYPE         0        10          2         23
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 41(18Q12.2) MUTATED           40       53        21         1
  DEL PEAK 41(18Q12.2) WILD-TYPE         15       10         3         1
D65V4, multiclass
            clus
vv           DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  STAGE I                              60                             44
  STAGE IA                              0                              1
  STAGE II                             22                             15
  STAGE IIA                           105                             67
  STAGE IIB                             5                              7
  STAGE IIC                             2                              0
  STAGE III                            14                             10
  STAGE IIIA                           13                              2
  STAGE IIIB                           61                             23
  STAGE IIIC                           40                             15
  STAGE IV                             53                             10
  STAGE IVA                            21                              3
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 41(18Q12.2) MUTATED    11  67 290  44
  DEL PEAK 41(18Q12.2) WILD-TYPE   9  38 127  25
D65V5, multiclass
    clus
vv   DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  T1                           11                              9
  T2                           67                             38
  T3                          290                            127
  T4                           44                             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 41(18Q12.2) MUTATED   208 116  87
  DEL PEAK 41(18Q12.2) WILD-TYPE 138  34  28
D65V6, multiclass
    clus
vv   DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  N0                          208                            138
  N1                          116                             34
  N2                           87                             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"
D65V7, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q12.2) MUTATED   295  74
  DEL PEAK 41(18Q12.2) WILD-TYPE 158  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED    295   74
  DEL PEAK 41(18Q12.2) WILD-TYPE  158   14
   clus
vv  DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  0                          295                            158
  1                           74                             14
[1] 2 2
[1] FALSE
D65V8, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q12.2) MUTATED   187 227
  DEL PEAK 41(18Q12.2) WILD-TYPE 102  98
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED    187  227
  DEL PEAK 41(18Q12.2) WILD-TYPE  102   98
        clus
vv       DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  FEMALE                          187                            102
  MALE                            227                             98
[1] 2 2
[1] FALSE
D65V9, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q12.2) MUTATED   322  24
  DEL PEAK 41(18Q12.2) WILD-TYPE 160   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED    322   24
  DEL PEAK 41(18Q12.2) WILD-TYPE  160    5
     clus
vv    DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  NO                           322                            160
  YES                           24                              5
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 41(18Q12.2) MUTATED                    255
  DEL PEAK 41(18Q12.2) WILD-TYPE                  127
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 41(18Q12.2) MUTATED                              14
  DEL PEAK 41(18Q12.2) WILD-TYPE                            48
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 41(18Q12.2) MUTATED                     128
  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
D65V10, multiclass
                                clus
vv                               DEL PEAK 41(18Q12.2) MUTATED
  COLON ADENOCARCINOMA                                    255
  COLON MUCINOUS ADENOCARCINOMA                            14
  RECTAL ADENOCARCINOMA                                   128
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 41(18Q12.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      127
  COLON MUCINOUS ADENOCARCINOMA                              48
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 41(18Q12.2) MUTATED   297   4  29  14
  DEL PEAK 41(18Q12.2) WILD-TYPE 149   2   8  15
D65V11, multiclass
    clus
vv   DEL PEAK 41(18Q12.2) MUTATED DEL PEAK 41(18Q12.2) WILD-TYPE
  R0                          297                            149
  R1                            4                              2
  R2                           29                              8
  RX                           14                             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
D65V13, binary
                                cls
clus                               0   1
  DEL PEAK 41(18Q12.2) MUTATED     4 237
  DEL PEAK 41(18Q12.2) WILD-TYPE   1 115
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 41(18Q12.2) MUTATED      4  237
  DEL PEAK 41(18Q12.2) WILD-TYPE    1  115
                        clus
vv                       DEL PEAK 41(18Q12.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          237
                        clus
vv                       DEL PEAK 41(18Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            115
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 42(18Q21.2) MUTATION ANALYSIS
D66V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 42(18Q21.2) MUTATED   331  87
  DEL PEAK 42(18Q21.2) WILD-TYPE 135  41
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                           418                            176 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                            87                             41 
$`DEL PEAK 42(18Q21.2) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        13.94        14.53         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       37.05        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 
       50.99        26.01        24.00        21.99        15.52       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 
       35.93        91.79        17.85        10.39        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        25.97        15.95        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       12.66         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        36.53        32.45        32.91        31.63 
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-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       27.09        22.52        24.13        25.18        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.39        23.87        20.28        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 
        5.03         7.04         1.02        37.05         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        9.07        19.07        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       33.99        21.01        24.00        13.94        61.02        78.08 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        5.98        37.05        25.02        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       17.03        10.06        33.07         0.99        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3968 
       27.02        18.05        24.00        20.98        34.03        21.99 
TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-A00D 
       16.08        13.05        34.06        27.02         7.96        19.00 
TCGA-AA-A00F TCGA-AA-A00K TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A017 
       34.03        18.05        42.02        17.03        14.99        15.02 
TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S TCGA-AA-A01T 
       15.02        10.98        32.02        31.00         1.02        33.04 
TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02J 
       26.01        37.02         2.96        39.98         2.01         5.03 
TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 
        0.92        41.00        40.96        24.53         5.79        22.42 
TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 TCGA-AY-4070 
       27.42        26.47        16.44         0.46        14.50        16.31 
TCGA-AY-5543 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
       33.01        17.82        17.26        17.85        18.84       109.28 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.65         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-4948 
       12.46        12.59        12.59        12.20        14.30       148.01 
TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 
       21.99         2.01        25.02         8.02        27.02        13.02 
TCGA-CM-5341 TCGA-CM-5344 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-5868 
       29.06        22.03        30.08         5.03        15.02        17.03 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6169 TCGA-CM-6170 
       14.04        29.03        16.04        21.99        13.02        15.02 
TCGA-CM-6172 TCGA-CM-6675 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 
       11.01        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        45.40        54.61        19.59        56.09        55.92 
TCGA-D5-6529 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6536 TCGA-D5-6538 
       20.19        17.75        18.25        25.48        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04        13.41        11.38        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
       44.32       131.51       139.17        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        31.96 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       11.11        35.74         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
       33.67        13.25         0.53        47.41         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 
       74.56        65.85        44.68        55.04        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6322 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U 
       36.00        26.04        46.75        74.79        18.18        10.98 
TCGA-NH-A50V TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX 
       19.33         9.93        12.79        16.80        42.77        32.98 
TCGA-QG-A5Z1 TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 
        8.42        21.90        38.70        60.13        11.90        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        29.98        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        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-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
       34.03        34.03         2.01        50.04         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       36.95        35.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       19.99        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02         1.02         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 
       38.56        43.20        27.55        26.43         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        12.62       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         3.48         4.18        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-EI-7004 
       16.41        11.51        10.78        13.64        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        42.35        28.57         0.39        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        11.87        12.46        47.08 

$`DEL PEAK 42(18Q21.2) WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       24.16        58.03        13.02         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00L 
        0.92        19.04        19.04        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 
       39.06        21.37        25.08        10.88        75.95       100.01 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-A015 
       22.09        35.80        26.17        79.69         8.02        36.03 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 
        9.53        46.65        42.90        32.75        33.53        22.06 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        25.08        24.69        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
       24.92         3.02        35.01        63.98         1.02         1.02 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3675 
        0.00        29.00        29.95        20.98         6.97        47.05 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
        1.02        17.98        15.95         0.00         0.00         0.00 
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-3966 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A004 TCGA-AA-A00A 
       26.01         2.01        25.02        27.02        13.94        38.04 
TCGA-AA-A00E TCGA-AA-A00J TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 
       30.02        18.05         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         1.02 
TCGA-AA-A029 TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 
       51.98        22.03        39.98        18.05        12.16        83.24 
TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-A71X 
        0.92        27.09         0.95         0.20        21.44        19.33 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5255 
       58.39         1.41        32.94        49.41         6.77        12.36 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 
       12.39        12.76        10.06        17.56        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 
       15.62        51.32        21.14        82.95       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        32.02        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        43.27        15.12         4.80        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        13.35        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        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 
        6.18        47.87        35.31       133.18        67.30        53.62 
TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GB TCGA-QG-A5YW 
       85.48        26.43        13.78        19.33        15.65        29.46 
TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 
       31.30        70.03        16.83        12.03        19.99         0.99 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 
       13.02        14.01        20.98        49.97        61.97         2.50 
TCGA-AH-6903 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 
       19.46        32.61        19.96         8.61        17.46         9.96 
TCGA-F5-6814 TCGA-F5-6861 
       37.18        38.14 

  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                          0.39                           0.00 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                        148.01                         135.65 
  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE 
                         23.01                          20.27 
[1] "0.4 - 148.0 (23.0)" "0.0 - 135.7 (20.3)"
[1] "hr=" "1.1"
D66V2, continuous
D66V3, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED   286 142
  DEL PEAK 42(18Q21.2) WILD-TYPE 162  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED    286  142
  DEL PEAK 42(18Q21.2) WILD-TYPE  162   20
        clus
vv       DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  COLON                           286                            162
  RECTUM                          142                             20
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 42(18Q21.2) MUTATED        62        0       24       107         5
  DEL PEAK 42(18Q21.2) WILD-TYPE      42        1       13        65         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 42(18Q21.2) MUTATED           2        15         13         64
  DEL PEAK 42(18Q21.2) WILD-TYPE         0         9          2         20
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 42(18Q21.2) MUTATED           43       56        22         2
  DEL PEAK 42(18Q21.2) WILD-TYPE         12        7         2         0
D66V4, multiclass
            clus
vv           DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  STAGE I                              62                             42
  STAGE IA                              0                              1
  STAGE II                             24                             13
  STAGE IIA                           107                             65
  STAGE IIB                             5                              7
  STAGE IIC                             2                              0
  STAGE III                            15                              9
  STAGE IIIA                           13                              2
  STAGE IIIB                           64                             20
  STAGE IIIC                           43                             12
  STAGE IV                             56                              7
  STAGE IVA                            22                              2
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 42(18Q21.2) MUTATED    12  68 301  48
  DEL PEAK 42(18Q21.2) WILD-TYPE   8  37 116  21
D66V5, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  T1                           12                              8
  T2                           68                             37
  T3                          301                            116
  T4                           48                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 42(18Q21.2) MUTATED   214 120  94
  DEL PEAK 42(18Q21.2) WILD-TYPE 132  30  21
D66V6, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  N0                          214                            132
  N1                          120                             30
  N2                           94                             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"
D66V7, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED   305  79
  DEL PEAK 42(18Q21.2) WILD-TYPE 148   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED    305   79
  DEL PEAK 42(18Q21.2) WILD-TYPE  148    9
   clus
vv  DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  0                          305                            148
  1                           79                              9
[1] 2 2
[1] FALSE
D66V8, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED   192 239
  DEL PEAK 42(18Q21.2) WILD-TYPE  97  86
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED    192  239
  DEL PEAK 42(18Q21.2) WILD-TYPE   97   86
        clus
vv       DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  FEMALE                          192                             97
  MALE                            239                             86
[1] 2 2
[1] FALSE
D66V9, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED   335  25
  DEL PEAK 42(18Q21.2) WILD-TYPE 147   4
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED    335   25
  DEL PEAK 42(18Q21.2) WILD-TYPE  147    4
     clus
vv    DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  NO                           335                            147
  YES                           25                              4
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                    267
  DEL PEAK 42(18Q21.2) WILD-TYPE                  115
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                              16
  DEL PEAK 42(18Q21.2) WILD-TYPE                            46
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                     129
  DEL PEAK 42(18Q21.2) WILD-TYPE                    17
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 42(18Q21.2) MUTATED                               11
  DEL PEAK 42(18Q21.2) WILD-TYPE                              2
D66V10, multiclass
                                clus
vv                               DEL PEAK 42(18Q21.2) MUTATED
  COLON ADENOCARCINOMA                                    267
  COLON MUCINOUS ADENOCARCINOMA                            16
  RECTAL ADENOCARCINOMA                                   129
  RECTAL MUCINOUS ADENOCARCINOMA                           11
                                clus
vv                               DEL PEAK 42(18Q21.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      115
  COLON MUCINOUS ADENOCARCINOMA                              46
  RECTAL ADENOCARCINOMA                                      17
  RECTAL MUCINOUS ADENOCARCINOMA                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 42(18Q21.2) MUTATED   307   4  30  15
  DEL PEAK 42(18Q21.2) WILD-TYPE 139   2   7  14
D66V11, multiclass
    clus
vv   DEL PEAK 42(18Q21.2) MUTATED DEL PEAK 42(18Q21.2) WILD-TYPE
  R0                          307                            139
  R1                            4                              2
  R2                           30                              7
  RX                           15                             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"
D66V12, continuous
D66V13, binary
                                cls
clus                               0   1
  DEL PEAK 42(18Q21.2) MUTATED     4 251
  DEL PEAK 42(18Q21.2) WILD-TYPE   1 101
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 42(18Q21.2) MUTATED      4  251
  DEL PEAK 42(18Q21.2) WILD-TYPE    1  101
                        clus
vv                       DEL PEAK 42(18Q21.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          251
                        clus
vv                       DEL PEAK 42(18Q21.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            101
[1] 2 2
[1] FALSE

Clustering(67) Variable = DEL PEAK 43(18Q22.1) MUTATION ANALYSIS
D67V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 43(18Q22.1) MUTATED   326  87
  DEL PEAK 43(18Q22.1) WILD-TYPE 140  41
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                           413                            181 
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                            87                             41 
$`DEL PEAK 43(18Q22.1) MUTATED`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3520 
       24.33        45.60        13.94        14.53         1.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 
       37.05        36.03        19.07        34.03        13.02        23.01 
TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3697 
       19.99        19.99         6.05        19.00        36.00        85.05 
TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3952 
       14.93        31.07        24.03        29.98        12.99         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-A00Z TCGA-AD-6888 TCGA-AZ-4681 
       50.99        26.01        24.00        21.99        15.52       106.75 
TCGA-AZ-6608 TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
        1.94        49.08         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 
       35.93        91.79        17.85        10.39        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        25.97        15.95        31.00        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-3L-AA1B TCGA-4N-A93T 
       21.24        18.28        55.76        26.43        15.62         4.80 
TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2675 
       12.66         1.61        39.45        43.76        43.76        43.43 
TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 
       42.28        44.91        35.11        16.57        37.05        37.25 
TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       37.02        34.65        36.53        32.45        32.91        31.63 
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-A6-6138 TCGA-A6-6140 TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 
       27.09        22.52        24.13        25.18        20.61        21.76 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       24.39        23.87        20.28        61.84        56.25         9.63 
TCGA-AA-3488 TCGA-AA-3489 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3511 TCGA-AA-3517 
        5.03         7.04         1.02        37.05         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 TCGA-AA-3544 
        9.07        19.07        29.00        26.01        12.99        14.01 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 
       33.99        21.01        24.00        13.94        61.02        78.08 
TCGA-AA-3664 TCGA-AA-3666 TCGA-AA-3667 TCGA-AA-3673 TCGA-AA-3678 TCGA-AA-3679 
       54.02         2.01        14.01        50.04        47.01        15.02 
TCGA-AA-3681 TCGA-AA-3685 TCGA-AA-3819 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 
        5.98        37.05        25.02        38.99        36.95        37.02 
TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       17.03        10.06        33.07         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3956 
       17.03        27.02        18.05        24.00        20.98        34.03 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3982 TCGA-AA-3989 
       21.99        16.08        13.05        34.06        27.02         7.96 
TCGA-AA-A004 TCGA-AA-A00D TCGA-AA-A00F TCGA-AA-A00Q TCGA-AA-A00U TCGA-AA-A00W 
       13.94        19.00        34.03        42.02        17.03        14.99 
TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01S 
       15.02        15.02        10.98        32.02        31.00         1.02 
TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02F TCGA-AA-A02H 
       33.04        26.01        37.02         2.96        39.98         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6890 TCGA-AD-6899 
        5.03         0.92        41.00        40.96        24.53         5.79 
TCGA-AD-6901 TCGA-AD-6963 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AM-5820 TCGA-AU-3779 
       22.42        27.42        26.47        16.44         0.46        14.50 
TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A8YK TCGA-AZ-4308 
       16.31        33.01        17.26        17.85        18.84       109.28 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 TCGA-AZ-5407 
        5.65         5.13        22.36        65.00        62.79        88.21 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 
       12.10        29.56         5.23        11.74         3.19        12.69 
TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-5914 
       12.46        12.59        12.59        12.20        14.30        21.99 
TCGA-CK-6748 TCGA-CM-4747 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5341 
        2.01        25.02         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-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 
       45.40        54.61        19.59        56.09        55.92        20.19 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6533 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25        25.48        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6541 TCGA-D5-6898 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 
       12.49        15.58         7.53        10.13        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 
        9.04        13.41        11.38        24.43        38.20       130.65 
TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA 
       92.75        49.91        13.32        12.59       140.38         7.50 
TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28A TCGA-DM-A28E 
       44.32       131.51       139.17        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        31.96 
TCGA-F4-6461 TCGA-F4-6569 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 
       11.11        35.74         1.55        34.42        41.42        43.04 
TCGA-F4-6808 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6297 
       33.67        13.25         0.53        47.41         8.35        82.39 
TCGA-G4-6299 TCGA-G4-6303 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6311 TCGA-G4-6315 
       74.56        65.85        44.68        55.04        39.42        61.91 
TCGA-G4-6317 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V 
       36.00        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV TCGA-QG-A5YX TCGA-QG-A5Z1 
        9.93        12.79        16.80        42.77        32.98         8.42 
TCGA-QL-A97D TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2687 TCGA-AF-2689 
       21.90        38.70        60.13        11.90        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       29.98        24.36        20.02        24.59        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 
        2.01        50.04         6.05         0.99        15.95        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        7.99         0.99        29.98        32.98         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 
       19.99         1.02        17.95        36.95        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02         3.98        46.03        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 
       23.01        37.02         9.07         1.02         1.02         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        38.56        43.20        27.55 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       26.43         6.05        33.17        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05       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         3.48         4.18        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        49.51        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        11.87        12.46        47.08 

$`DEL PEAK 43(18Q22.1) WILD-TYPE`
TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3554 
       24.16        58.03        13.02         8.05         0.99        17.95 
TCGA-AA-3672 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3950 TCGA-AA-3986 TCGA-AA-A00L 
        0.92        19.04        19.04        24.00        19.07        38.04 
TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 
       39.06        21.37        25.08        10.88        75.95       100.01 
TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6628 TCGA-AG-3580 TCGA-AG-A015 
       22.09        35.80        26.17        79.69         8.02        36.03 
TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2676 TCGA-A6-3809 TCGA-A6-5661 TCGA-A6-5665 
        9.53        46.65        42.90        32.75        33.53        22.06 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-A565 
        8.38        25.08        24.69        20.12        19.66        16.24 
TCGA-A6-A566 TCGA-AA-3492 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
       24.92         3.02        35.01        63.98         1.02         1.02 
TCGA-AA-3529 TCGA-AA-3534 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3663 TCGA-AA-3675 
        0.00        29.00        29.95        20.98         6.97        47.05 
TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 
       11.01         5.03        26.99        10.06        35.05         0.99 
TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 TCGA-AA-3852 
        1.02        17.98        15.95         0.00         0.00         0.00 
TCGA-AA-3854 TCGA-AA-3855 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 
       36.03        32.05        31.00         2.01        33.01        26.01 
TCGA-AA-3966 TCGA-AA-3977 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00E TCGA-AA-A00J 
        2.01        25.02        27.02        38.04        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00O TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A01G 
       18.05         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-A029 
       31.00        38.07         1.02        35.01         1.02        51.98 
TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 TCGA-AD-6889 TCGA-AM-5821 
       22.03        39.98        18.05        12.16        83.24         0.92 
TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A71X 
       27.09         0.95         0.20        21.44        17.82        19.33 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4615 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-CA-5255 
       58.39         1.41        32.94        49.41         6.77        12.36 
TCGA-CA-5796 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 
       12.39        12.76        10.06        17.56       148.01        85.45 
TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 
       70.16        15.62        51.32        21.14        82.95       124.27 
TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 TCGA-CM-5348 TCGA-CM-5860 
       23.05        20.02        37.02        26.04        22.98        32.02 
TCGA-CM-5861 TCGA-CM-5863 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6167 TCGA-CM-6168 
       15.02        15.02        15.02        12.00        14.99        12.99 
TCGA-CM-6171 TCGA-CM-6674 TCGA-D5-6530 TCGA-D5-6534 TCGA-D5-6537 TCGA-D5-6540 
       14.04        12.95        20.42        43.27         4.80        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        13.35        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        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6302 TCGA-G4-6304 
        6.18        47.87        35.31       133.18        67.30        53.62 
TCGA-G4-6309 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-NH-A5IV TCGA-NH-A6GB 
       85.48        26.43        26.04        13.78        19.33        15.65 
TCGA-QG-A5YW TCGA-QG-A5Z2 TCGA-WS-AB45 TCGA-AF-5654 TCGA-AG-3586 TCGA-AG-3599 
       29.46        31.30        70.03        16.83         1.02        12.03 
TCGA-AG-3609 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 
       19.99        37.02         0.99        13.02        14.01        20.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6621 TCGA-DT-5265 
       49.97        61.97         2.50        19.46        13.78        12.62 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 
       32.61        19.96         8.61        17.46         9.96        37.18 
TCGA-F5-6861 
       38.14 

  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                          0.39                           0.00 
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE 
                         23.01                          20.12 
[1] "0.4 - 140.4 (23.0)" "0.0 - 148.0 (20.1)"
[1] "hr=" "1.1"
D67V2, continuous
D67V3, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q22.1) MUTATED   285 138
  DEL PEAK 43(18Q22.1) WILD-TYPE 163  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.1) MUTATED    285  138
  DEL PEAK 43(18Q22.1) WILD-TYPE  163   24
        clus
vv       DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  COLON                           285                            163
  RECTUM                          138                             24
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 43(18Q22.1) MUTATED        62        0       24       107         5
  DEL PEAK 43(18Q22.1) WILD-TYPE      42        1       13        65         7
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 43(18Q22.1) MUTATED           2        13         13         62
  DEL PEAK 43(18Q22.1) WILD-TYPE         0        11          2         22
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 43(18Q22.1) MUTATED           43       55        22         2
  DEL PEAK 43(18Q22.1) WILD-TYPE         12        8         2         0
D67V4, multiclass
            clus
vv           DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  STAGE I                              62                             42
  STAGE IA                              0                              1
  STAGE II                             24                             13
  STAGE IIA                           107                             65
  STAGE IIB                             5                              7
  STAGE IIC                             2                              0
  STAGE III                            13                             11
  STAGE IIIA                           13                              2
  STAGE IIIB                           62                             22
  STAGE IIIC                           43                             12
  STAGE IV                             55                              8
  STAGE IVA                            22                              2
  STAGE IVB                             2                              0
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 43(18Q22.1) MUTATED    12  68 296  48
  DEL PEAK 43(18Q22.1) WILD-TYPE   8  37 121  21
D67V5, multiclass
    clus
vv   DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  T1                           12                              8
  T2                           68                             37
  T3                          296                            121
  T4                           48                             21
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 43(18Q22.1) MUTATED   214 116  93
  DEL PEAK 43(18Q22.1) WILD-TYPE 132  34  22
D67V6, multiclass
    clus
vv   DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  N0                          214                            132
  N1                          116                             34
  N2                           93                             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q22.1) MUTATED   302  78
  DEL PEAK 43(18Q22.1) WILD-TYPE 151  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.1) MUTATED    302   78
  DEL PEAK 43(18Q22.1) WILD-TYPE  151   10
   clus
vv  DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  0                          302                            151
  1                           78                             10
[1] 2 2
[1] FALSE
D67V8, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q22.1) MUTATED   190 236
  DEL PEAK 43(18Q22.1) WILD-TYPE  99  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.1) MUTATED    190  236
  DEL PEAK 43(18Q22.1) WILD-TYPE   99   89
        clus
vv       DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  FEMALE                          190                             99
  MALE                            236                             89
[1] 2 2
[1] FALSE
D67V9, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q22.1) MUTATED   334  24
  DEL PEAK 43(18Q22.1) WILD-TYPE 148   5
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.1) MUTATED    334   24
  DEL PEAK 43(18Q22.1) WILD-TYPE  148    5
     clus
vv    DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  NO                           334                            148
  YES                           24                              5
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 43(18Q22.1) MUTATED                    267
  DEL PEAK 43(18Q22.1) WILD-TYPE                  115
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 43(18Q22.1) MUTATED                              15
  DEL PEAK 43(18Q22.1) WILD-TYPE                            47
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 43(18Q22.1) MUTATED                     127
  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
D67V10, multiclass
                                clus
vv                               DEL PEAK 43(18Q22.1) MUTATED
  COLON ADENOCARCINOMA                                    267
  COLON MUCINOUS ADENOCARCINOMA                            15
  RECTAL ADENOCARCINOMA                                   127
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 43(18Q22.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      115
  COLON MUCINOUS ADENOCARCINOMA                              47
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 43(18Q22.1) MUTATED   304   4  29  15
  DEL PEAK 43(18Q22.1) WILD-TYPE 142   2   8  14
D67V11, multiclass
    clus
vv   DEL PEAK 43(18Q22.1) MUTATED DEL PEAK 43(18Q22.1) WILD-TYPE
  R0                          304                            142
  R1                            4                              2
  R2                           29                              8
  RX                           15                             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
D67V13, binary
                                cls
clus                               0   1
  DEL PEAK 43(18Q22.1) MUTATED     4 247
  DEL PEAK 43(18Q22.1) WILD-TYPE   1 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 43(18Q22.1) MUTATED      4  247
  DEL PEAK 43(18Q22.1) WILD-TYPE    1  105
                        clus
vv                       DEL PEAK 43(18Q22.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          247
                        clus
vv                       DEL PEAK 43(18Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            105
[1] 2 2
[1] FALSE

Clustering(68) Variable = DEL PEAK 44(19P13.3) MUTATION ANALYSIS
D68V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 44(19P13.3) MUTATED    68  24
  DEL PEAK 44(19P13.3) WILD-TYPE 398 104
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            92                            502 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                            24                            104 
$`DEL PEAK 44(19P13.3) MUTATED`
TCGA-AA-3506 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3692 
       58.03        13.02        23.01        19.99         6.05        36.00 
TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3979 TCGA-CK-5912 
       31.07        24.03         2.01        50.99        24.00        49.08 
TCGA-AG-3611 TCGA-AG-4008 TCGA-AG-A014 TCGA-G5-6233 TCGA-4N-A93T TCGA-A6-3807 
       13.94        17.03        15.95        18.28         4.80        34.65 
TCGA-A6-6142 TCGA-A6-6651 TCGA-A6-A567 TCGA-AA-3519 TCGA-AA-3538 TCGA-AA-3542 
       25.08        21.76        61.84         9.07        26.01        12.99 
TCGA-AA-3666 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3850 TCGA-AA-3866 TCGA-AA-3869 
        2.01        36.95        37.02         0.00        17.03        27.02 
TCGA-AA-3941 TCGA-AA-A00O TCGA-AA-A01D TCGA-AA-A01G TCGA-AA-A01T TCGA-AA-A01X 
       24.00        27.02        10.98        12.00        33.04        26.01 
TCGA-AA-A02F TCGA-AA-A02W TCGA-AD-6901 TCGA-AD-6965 TCGA-AY-4070 TCGA-AY-6196 
       39.98        41.00        22.42        26.47        16.31         0.20 
TCGA-AZ-4616 TCGA-AZ-4684 TCGA-CA-5797 TCGA-CK-4948 TCGA-CM-6169 TCGA-CM-6675 
        5.13        65.00        12.59       148.01        13.02        13.05 
TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-6529 TCGA-D5-6533 TCGA-D5-6537 TCGA-D5-6541 
       10.06        45.40        20.19        25.48         4.80        15.58 
TCGA-D5-6922 TCGA-DM-A0X9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-F4-6461 TCGA-F4-6808 
       10.13       119.70        44.32       131.51        11.11        33.67 
TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6317 TCGA-NH-A50U TCGA-RU-A8FL TCGA-SS-A7HO 
        8.35        82.39        36.00        10.98        38.70        60.13 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-4110 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3608 
       46.92        39.48        29.98        12.00        36.03        15.95 
TCGA-AG-3725 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3893 TCGA-AG-A016 TCGA-CI-6619 
       20.98        32.98        19.04        35.01         9.07         6.05 
TCGA-CI-6620 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE 
       33.17        31.00        13.97        10.98        12.62       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6885 TCGA-F5-6571 
       24.13        51.48        17.00        16.34        13.64        42.35 
TCGA-F5-6702 TCGA-F5-6810 
       28.57         0.39 

$`DEL PEAK 44(19P13.3) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-A6-6649 TCGA-AA-3496 
       24.33        45.60        13.94        14.53        24.16         1.02 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 
       13.02        24.03        37.05        36.03         8.05        19.07 
TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3560 TCGA-AA-3672 TCGA-AA-3688 
       34.03         0.99        17.95        19.99         0.92        19.00 
TCGA-AA-3697 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3870 TCGA-AA-3939 
       85.05        19.04        19.04        14.93        29.98        12.99 
TCGA-AA-3950 TCGA-AA-3976 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 
       24.00        26.01        19.07        38.04        21.99        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-AZ-6608 TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 
      100.01         1.94         5.88        28.21        23.51        63.62 
TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 TCGA-G4-6625 TCGA-G4-6628 
       35.93        22.09        35.80        26.17        91.79        79.69 
TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H 
       17.85        10.39         8.02        19.99        17.03        25.97 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 
       36.03        31.00        51.98        21.24        55.76        26.43 
TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 
       15.62        12.66         1.61         9.53        39.45        43.76 
TCGA-A6-2672 TCGA-A6-2674 TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 
       46.65        43.76        43.43        42.90        42.28        44.91 
TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       35.11        16.57        37.05        37.25        37.02        32.75 
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-A6-5664 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-A6-6650 
       27.09        22.52        24.13         8.38        25.18        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        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3517 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 
        1.02        38.99         1.02        19.07         0.00        29.00 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3553 TCGA-AA-3555 
       29.00        14.01        33.99        21.01        24.00        29.95 
TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 
       20.98        13.94        61.02        78.08         6.97        54.02 
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-3685 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3811 TCGA-AA-3812 
        5.98        37.05         5.03        26.99        10.06        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-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03        10.06        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3875 TCGA-AA-3877 
       32.05         0.99        31.07        53.00        18.05        31.00 
TCGA-AA-3930 TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3966 
        2.01        33.01        26.01        20.98        34.03         2.01 
TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 
       21.99        16.08        13.05        34.06        25.02        27.02 
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-A00Q TCGA-AA-A00R 
       34.03        18.05        18.05         4.01        42.02         0.99 
TCGA-AA-A00U TCGA-AA-A00W TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01C TCGA-AA-A01F 
       17.03        14.99        34.98        15.02        15.02        32.02 
TCGA-AA-A01I TCGA-AA-A01K TCGA-AA-A01P TCGA-AA-A01Q TCGA-AA-A01R TCGA-AA-A01S 
       31.00        31.00        38.07         1.02        35.01         1.02 
TCGA-AA-A01V TCGA-AA-A01Z TCGA-AA-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-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 
        0.92        22.03        39.98        18.05        40.96        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6963 TCGA-AD-A5EK TCGA-AM-5820 
       83.24        24.53         5.79        27.42        16.44         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        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4308 
       17.82        17.26        17.85        19.33        18.84       109.28 
TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 
       58.39         1.41         5.65        32.94        22.36        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 
       88.21        49.41         6.77        12.10        29.56         5.23 
TCGA-AZ-6606 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 TCGA-CA-5796 
       11.74         3.19        12.69        12.36        12.46        12.39 
TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 
       12.59        12.20        12.76        10.06        14.30        17.56 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       82.95         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 
       25.02        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        32.02        15.02         5.03 
TCGA-CM-5863 TCGA-CM-5864 TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 
       15.02        15.02        17.03        15.02        12.00        14.04 
TCGA-CM-6164 TCGA-CM-6165 TCGA-CM-6166 TCGA-CM-6167 TCGA-CM-6168 TCGA-CM-6170 
       29.03        16.04        21.99        14.99        12.99        15.02 
TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6676 TCGA-CM-6677 TCGA-CM-6678 
       14.04        11.01        12.95        11.08        11.08        11.01 
TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 TCGA-D5-5541 TCGA-D5-6530 
       12.03        54.61        19.59        56.09        55.92        20.42 
TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6538 
       17.75        18.25        43.27        15.12        17.85        17.13 
TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6923 TCGA-D5-6924 
       12.49        16.14         7.53        12.39        12.43        14.30 
TCGA-D5-6926 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6929 TCGA-D5-6930 TCGA-D5-6931 
        9.04         9.44        11.64        13.41        13.35        12.00 
TCGA-D5-6932 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       11.38        10.26        24.43        38.20       130.65        92.75 
TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D8 TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HB 
       49.91        13.32        12.59       140.38         7.50       135.65 
TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-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-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 
       31.96        35.74        35.74         6.18        47.87         1.55 
TCGA-F4-6805 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6809 TCGA-F4-6854 TCGA-F4-6855 
       34.42        41.42        43.04        13.25         0.53        47.41 
TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
       35.31       133.18        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6315 TCGA-G4-6320 
       44.68        55.04        85.48        39.42        61.91        26.43 
TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50V 
       26.04        13.78        46.75        74.79        18.18        19.33 
TCGA-NH-A5IV TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YV 
       19.33         9.93        15.65        12.79        16.80        42.77 
TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-T9-A92H 
       29.46        32.98         8.42        31.30        21.90        11.90 
TCGA-WS-AB45 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       70.03        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        16.83        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 
       65.98        11.84        36.03        32.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       24.00         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 
        2.01        50.04        12.03         6.05         0.99        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        37.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       19.99         1.02        17.95        36.95        13.02        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        23.01        37.02         1.02         1.02 
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 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       21.01        25.05        26.04        12.00        31.00        51.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       44.02        25.97        25.05        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       57.24        32.61         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 
       20.91        18.28        15.85        17.69        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        11.51        10.78        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        49.51        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                             0                              0 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                        148.01                         140.38 
  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE 
                        23.505                         21.990 
[1] "0.0 - 148.0 (23.5)" "0.0 - 140.4 (22.0)"
[1] "hr=" "1.2"
D68V2, continuous
D68V3, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    63  33
  DEL PEAK 44(19P13.3) WILD-TYPE 385 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     63   33
  DEL PEAK 44(19P13.3) WILD-TYPE  385  129
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  COLON                            63                            385
  RECTUM                           33                            129
[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         1
  DEL PEAK 44(19P13.3) WILD-TYPE      93        1       33       154        11
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 44(19P13.3) MUTATED           0         6          3          9
  DEL PEAK 44(19P13.3) WILD-TYPE         2        18         12         75
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 44(19P13.3) MUTATED           16       15         8         1
  DEL PEAK 44(19P13.3) WILD-TYPE         39       48        16         1
D68V4, multiclass
            clus
vv           DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  STAGE I                              11                             93
  STAGE IA                              0                              1
  STAGE II                              4                             33
  STAGE IIA                            18                            154
  STAGE IIB                             1                             11
  STAGE IIC                             0                              2
  STAGE III                             6                             18
  STAGE IIIA                            3                             12
  STAGE IIIB                            9                             75
  STAGE IIIC                           16                             39
  STAGE IV                             15                             48
  STAGE IVA                             8                             16
  STAGE IVB                             1                              1
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 44(19P13.3) MUTATED     1  13  70  12
  DEL PEAK 44(19P13.3) WILD-TYPE  19  92 347  57
D68V5, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  T1                            1                             19
  T2                           13                             92
  T3                           70                            347
  T4                           12                             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 44(19P13.3) MUTATED    36  28  32
  DEL PEAK 44(19P13.3) WILD-TYPE 310 122  83
D68V6, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  N0                           36                            310
  N1                           28                            122
  N2                           32                             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"
D68V7, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    64  23
  DEL PEAK 44(19P13.3) WILD-TYPE 389  65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     64   23
  DEL PEAK 44(19P13.3) WILD-TYPE  389   65
   clus
vv  DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  0                           64                            389
  1                           23                             65
[1] 2 2
[1] FALSE
D68V8, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    41  56
  DEL PEAK 44(19P13.3) WILD-TYPE 248 269
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     41   56
  DEL PEAK 44(19P13.3) WILD-TYPE  248  269
        clus
vv       DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  FEMALE                           41                            248
  MALE                             56                            269
[1] 2 2
[1] FALSE
D68V9, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED    77   3
  DEL PEAK 44(19P13.3) WILD-TYPE 405  26
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED     77    3
  DEL PEAK 44(19P13.3) WILD-TYPE  405   26
     clus
vv    DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  NO                            77                            405
  YES                            3                             26
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                     57
  DEL PEAK 44(19P13.3) WILD-TYPE                  325
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                               5
  DEL PEAK 44(19P13.3) WILD-TYPE                            57
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                      31
  DEL PEAK 44(19P13.3) WILD-TYPE                   115
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 44(19P13.3) MUTATED                                1
  DEL PEAK 44(19P13.3) WILD-TYPE                             12
D68V10, multiclass
                                clus
vv                               DEL PEAK 44(19P13.3) MUTATED
  COLON ADENOCARCINOMA                                     57
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    31
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 44(19P13.3) WILD-TYPE
  COLON ADENOCARCINOMA                                      325
  COLON MUCINOUS ADENOCARCINOMA                              57
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 44(19P13.3) MUTATED    64   2  10   4
  DEL PEAK 44(19P13.3) WILD-TYPE 382   4  27  25
D68V11, multiclass
    clus
vv   DEL PEAK 44(19P13.3) MUTATED DEL PEAK 44(19P13.3) WILD-TYPE
  R0                           64                            382
  R1                            2                              4
  R2                           10                             27
  RX                            4                             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"
D68V12, continuous
D68V13, binary
                                cls
clus                               0   1
  DEL PEAK 44(19P13.3) MUTATED     1  51
  DEL PEAK 44(19P13.3) WILD-TYPE   4 301
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 44(19P13.3) MUTATED      1   51
  DEL PEAK 44(19P13.3) WILD-TYPE    4  301
                        clus
vv                       DEL PEAK 44(19P13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           51
                        clus
vv                       DEL PEAK 44(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            301
[1] 2 2
[1] FALSE

Clustering(69) Variable = DEL PEAK 45(20P12.1) MUTATION ANALYSIS
D69V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 45(20P12.1) MUTATED    98  31
  DEL PEAK 45(20P12.1) WILD-TYPE 368  97
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                           129                            465 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                            31                             97 
$`DEL PEAK 45(20P12.1) MUTATED`
TCGA-A6-2677 TCGA-A6-4105 TCGA-AA-3496 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3697 
       24.33        14.53         1.02        34.03         0.99        85.05 
TCGA-AA-3867 TCGA-AA-3952 TCGA-AZ-6608 TCGA-G4-6298 TCGA-AF-3913 TCGA-AG-A01N 
       24.03         2.01         1.94        23.51        10.39        31.00 
TCGA-G5-6641 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-5667 TCGA-A6-6140 
       26.43        29.19        23.61        32.71        29.16        24.13 
TCGA-A6-6648 TCGA-A6-6650 TCGA-A6-6651 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3538 
       25.18        20.61        21.76        38.99         9.07        26.01 
TCGA-AA-3542 TCGA-AA-3553 TCGA-AA-3561 TCGA-AA-3660 TCGA-AA-3681 TCGA-AA-3819 
       12.99        24.00        13.94        78.08         5.98        25.02 
TCGA-AA-3841 TCGA-AA-3855 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-A00D TCGA-AA-A00F 
       36.95        32.05        20.98         2.01        19.00        34.03 
TCGA-AA-A00Q TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A01Q TCGA-AA-A01Z TCGA-AA-A02F 
       42.02        32.02        31.00         1.02        37.02        39.98 
TCGA-AA-A03J TCGA-AD-6965 TCGA-AY-5543 TCGA-AZ-4308 TCGA-AZ-5403 TCGA-AZ-6605 
       40.96        26.47        33.01       109.28        62.79         5.23 
TCGA-AZ-6606 TCGA-CK-4948 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-5344 TCGA-CM-5349 
       11.74       148.01        21.99         2.01        22.03        30.08 
TCGA-CM-6164 TCGA-CM-6168 TCGA-CM-6169 TCGA-CM-6170 TCGA-CM-6676 TCGA-D5-5540 
       29.03        12.99        13.02        15.02        11.08        56.09 
TCGA-D5-5541 TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A0X9 
       55.92        25.48        43.27        13.41        11.38       119.70 
TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1HA 
       38.20       130.65        92.75        49.91        13.32       131.51 
TCGA-DM-A28A TCGA-DM-A28E TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6809 
       26.47       119.93        41.42        43.04        33.67        13.25 
TCGA-F4-6854 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6320 TCGA-NH-A50V TCGA-NH-A8F8 
        0.53         8.35        61.91        26.43        19.33        16.80 
TCGA-QG-A5Z1 TCGA-RU-A8FL TCGA-SS-A7HO TCGA-T9-A92H TCGA-AF-2689 TCGA-AF-4110 
        8.42        38.70        60.13        11.90        39.48        29.98 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 
       86.63        65.98        11.84        36.03        32.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3742 TCGA-AG-3883 
       20.05        24.00         6.05        15.95         0.99         1.02 
TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G 
       32.02        46.03        13.94         1.02         1.94        38.96 
TCGA-AH-6547 TCGA-AH-6643 TCGA-CI-6624 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 
        2.50        43.20        48.20        12.00        10.98        44.02 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 
       25.05        41.36        57.24        24.13        32.61         4.18 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 
       15.85        17.69        16.41        11.51        10.78         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6864 
       42.35        28.57        12.46 

$`DEL PEAK 45(20P12.1) WILD-TYPE`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3520 
       45.60        13.94        24.16        58.03        13.02        24.03 
TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3552 TCGA-AA-3554 
       37.05        36.03         8.05        19.07        13.02        17.95 
TCGA-AA-3556 TCGA-AA-3560 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3688 
       23.01        19.99        19.99         6.05         0.92        19.00 
TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3870 
       36.00        19.04        19.04        14.93        31.07        29.98 
TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 
       12.99        24.00        50.99        26.01        24.00        19.07 
TCGA-AA-A00L TCGA-AA-A00Z TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 
       38.04        21.99        39.06        21.37        15.52        25.08 
TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-CK-5912 TCGA-DM-A285 
       10.88        75.95       106.75       100.01        49.08         5.88 
TCGA-G4-6294 TCGA-G4-6310 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 TCGA-G4-6588 
       28.21        63.62        35.93        22.09        35.80        26.17 
TCGA-G4-6625 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       91.79        79.69        17.85         8.02        13.94        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 
       17.03        17.03        25.97        15.95        36.03        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H 
       21.24        18.28        55.76        15.62         4.80        12.66 
TCGA-5M-AAT4 TCGA-5M-AAT6 TCGA-5M-AATE TCGA-A6-2671 TCGA-A6-2672 TCGA-A6-2674 
        1.61         9.53        39.45        43.76        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 
       43.43        42.90        42.28        44.91        35.11        16.57 
TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 
       37.05        37.25        37.02        34.65        32.75        36.53 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5661 TCGA-A6-5664 
       32.45        32.91        31.63        30.44        33.53        22.09 
TCGA-A6-5665 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6652 
       22.06        27.09        22.52         8.38        25.08        24.69 
TCGA-A6-6653 TCGA-A6-6654 TCGA-A6-6780 TCGA-A6-6781 TCGA-A6-6782 TCGA-A6-A565 
       24.39        23.87        20.12        19.66        20.28        16.24 
TCGA-A6-A566 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3489 
       24.92        61.84        56.25         9.63         5.03         7.04 
TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3511 
        3.02         1.02        37.05        35.01        63.98         6.97 
TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 
        1.02         1.02        19.07         0.00        29.00        29.00 
TCGA-AA-3544 TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 
       14.01        33.99        21.01        29.95        20.98        61.02 
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-3680 TCGA-AA-3685 TCGA-AA-3696 TCGA-AA-3710 
       47.01        15.02        11.01        37.05         5.03        26.99 
TCGA-AA-3811 TCGA-AA-3812 TCGA-AA-3818 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 
       10.06        35.05         0.99         1.02        17.98        15.95 
TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3848 TCGA-AA-3850 
       38.99        37.02         0.00        17.03        10.06         0.00 
TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3864 
       33.07         0.00        36.03         0.99        31.07        53.00 
TCGA-AA-3866 TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3941 
       17.03        27.02        18.05        31.00         2.01        24.00 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3968 TCGA-AA-3971 TCGA-AA-3973 
       33.01        26.01        34.03        21.99        16.08        13.05 
TCGA-AA-3975 TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3989 TCGA-AA-3994 TCGA-AA-A004 
       34.06        25.02        27.02         7.96        27.02        13.94 
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-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-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01R TCGA-AA-A01S 
       10.98        12.00        31.00        38.07        35.01         1.02 
TCGA-AA-A01T TCGA-AA-A01V TCGA-AA-A01X TCGA-AA-A029 TCGA-AA-A02E TCGA-AA-A02H 
       33.04         1.02        26.01        51.98         2.96         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-6889 TCGA-AD-6890 TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6963 
       12.16        83.24        24.53         5.79        22.42        27.42 
TCGA-AD-A5EK TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-3779 TCGA-AU-6004 TCGA-AY-4070 
       16.44         0.46         0.92        14.50        27.09        16.31 
TCGA-AY-4071 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A69D 
        0.95         0.20        21.44        17.82        17.26        17.85 
TCGA-AY-A71X TCGA-AY-A8YK TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       19.33        18.84        58.39         1.41         5.65        32.94 
TCGA-AZ-4616 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 
        5.13        22.36        65.00        88.21        49.41         6.77 
TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-5256 
       12.10        29.56         3.19        12.69        12.36        12.46 
TCGA-CA-5796 TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6716 TCGA-CA-6717 TCGA-CA-6718 
       12.39        12.59        12.59        12.20        12.76        10.06 
TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       14.30        17.56        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 
       21.14        82.95       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 
       25.02        26.04         8.02        27.02        13.02        29.06 
TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-5864 
       22.98        32.02        15.02         5.03        15.02        15.02 
TCGA-CM-5868 TCGA-CM-6161 TCGA-CM-6162 TCGA-CM-6163 TCGA-CM-6165 TCGA-CM-6166 
       17.03        15.02        12.00        14.04        16.04        21.99 
TCGA-CM-6167 TCGA-CM-6171 TCGA-CM-6172 TCGA-CM-6674 TCGA-CM-6675 TCGA-CM-6677 
       14.99        14.04        11.01        12.95        13.05        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        45.40        54.61        19.59 
TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6535 TCGA-D5-6536 
       20.19        20.42        17.75        18.25        15.12        17.85 
TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6898 
        4.80        17.13        12.49        16.14        15.58         7.53 
TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6927 
       12.39        10.13        12.43        14.30         9.04         9.44 
TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 TCGA-D5-7000 TCGA-DM-A0XD TCGA-DM-A1D8 
       11.64        13.35        12.00        10.26        24.43        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 
      140.38         7.50        44.32       135.65         7.76       139.17 
TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K 
       14.04        81.37        35.97        60.79       117.07        98.24 
TCGA-DM-A28M TCGA-F4-6459 TCGA-F4-6460 TCGA-F4-6461 TCGA-F4-6463 TCGA-F4-6569 
       95.18         8.61        31.96        11.11        35.74        35.74 
TCGA-F4-6570 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6805 TCGA-F4-6855 TCGA-F4-6856 
        6.18        47.87         1.55        34.42        47.41        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6317 TCGA-G4-6322 
       44.68        55.04        85.48        39.42        36.00        26.04 
TCGA-G4-6323 TCGA-G4-6626 TCGA-G4-6627 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A5IV 
       13.78        46.75        74.79        18.18        10.98        19.33 
TCGA-NH-A6GA TCGA-NH-A6GB TCGA-NH-A6GC TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QG-A5YX 
        9.93        15.65        12.79        42.77        29.46        32.98 
TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 
       31.30        21.90        70.03        46.92        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 
       13.55        37.97        34.49        37.74        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 
       20.02        24.59        12.00        36.03         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       37.02        32.98         0.99        19.04        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
        3.98        20.98         6.02        23.01        37.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.02        49.97        61.97        41.00        38.04        38.56 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       44.78        47.44        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
       26.04        31.00        13.97        31.00        51.98        25.97 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 
       25.05        12.62       126.44       129.27        51.48         3.48 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 
       20.55        19.96        20.91        17.00        18.28        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 
       16.31         8.61        13.64        17.46        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       49.51         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       38.14        11.87        47.08 

  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                          0.53                           0.00 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                        148.01                         140.38 
  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE 
                         25.02                          21.01 
[1] "0.5 - 148.0 (25.0)" "0.0 - 140.4 (21.0)"
[1] "hr=" "1"  
D69V2, continuous
D69V3, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED    86  48
  DEL PEAK 45(20P12.1) WILD-TYPE 362 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED     86   48
  DEL PEAK 45(20P12.1) WILD-TYPE  362  114
        clus
vv       DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  COLON                            86                            362
  RECTUM                           48                            114
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 45(20P12.1) MUTATED        17        0       12        33         1
  DEL PEAK 45(20P12.1) WILD-TYPE      87        1       25       139        11
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 45(20P12.1) MUTATED           2         4          5         21
  DEL PEAK 45(20P12.1) WILD-TYPE         0        20         10         63
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 45(20P12.1) MUTATED           16       14         7         0
  DEL PEAK 45(20P12.1) WILD-TYPE         39       49        17         2
D69V4, multiclass
            clus
vv           DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  STAGE I                              17                             87
  STAGE IA                              0                              1
  STAGE II                             12                             25
  STAGE IIA                            33                            139
  STAGE IIB                             1                             11
  STAGE IIC                             2                              0
  STAGE III                             4                             20
  STAGE IIIA                            5                             10
  STAGE IIIB                           21                             63
  STAGE IIIC                           16                             39
  STAGE IV                             14                             49
  STAGE IVA                             7                             17
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 45(20P12.1) MUTATED     3  20  97  15
  DEL PEAK 45(20P12.1) WILD-TYPE  17  85 320  54
D69V5, multiclass
    clus
vv   DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  T1                            3                             17
  T2                           20                             85
  T3                           97                            320
  T4                           15                             54
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 45(20P12.1) MUTATED    69  36  30
  DEL PEAK 45(20P12.1) WILD-TYPE 277 114  85
D69V6, multiclass
    clus
vv   DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  N0                           69                            277
  N1                           36                            114
  N2                           30                             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"
D69V7, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED   104  20
  DEL PEAK 45(20P12.1) WILD-TYPE 349  68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED    104   20
  DEL PEAK 45(20P12.1) WILD-TYPE  349   68
   clus
vv  DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  0                          104                            349
  1                           20                             68
[1] 2 2
[1] FALSE
D69V8, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED    67  68
  DEL PEAK 45(20P12.1) WILD-TYPE 222 257
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED     67   68
  DEL PEAK 45(20P12.1) WILD-TYPE  222  257
        clus
vv       DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  FEMALE                           67                            222
  MALE                             68                            257
[1] 2 2
[1] FALSE
D69V9, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED   102   4
  DEL PEAK 45(20P12.1) WILD-TYPE 380  25
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED    102    4
  DEL PEAK 45(20P12.1) WILD-TYPE  380   25
     clus
vv    DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  NO                           102                            380
  YES                            4                             25
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 45(20P12.1) MUTATED                     79
  DEL PEAK 45(20P12.1) WILD-TYPE                  303
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(20P12.1) MUTATED                               5
  DEL PEAK 45(20P12.1) WILD-TYPE                            57
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 45(20P12.1) MUTATED                      43
  DEL PEAK 45(20P12.1) WILD-TYPE                   103
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 45(20P12.1) MUTATED                                5
  DEL PEAK 45(20P12.1) WILD-TYPE                              8
D69V10, multiclass
                                clus
vv                               DEL PEAK 45(20P12.1) MUTATED
  COLON ADENOCARCINOMA                                     79
  COLON MUCINOUS ADENOCARCINOMA                             5
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 45(20P12.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      303
  COLON MUCINOUS ADENOCARCINOMA                              57
  RECTAL ADENOCARCINOMA                                     103
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 45(20P12.1) MUTATED    93   2   8   3
  DEL PEAK 45(20P12.1) WILD-TYPE 353   4  29  26
D69V11, multiclass
    clus
vv   DEL PEAK 45(20P12.1) MUTATED DEL PEAK 45(20P12.1) WILD-TYPE
  R0                           93                            353
  R1                            2                              4
  R2                            8                             29
  RX                            3                             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"
D69V12, continuous
D69V13, binary
                                cls
clus                               0   1
  DEL PEAK 45(20P12.1) MUTATED     1  81
  DEL PEAK 45(20P12.1) WILD-TYPE   4 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 45(20P12.1) MUTATED      1   81
  DEL PEAK 45(20P12.1) WILD-TYPE    4  271
                        clus
vv                       DEL PEAK 45(20P12.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           81
                        clus
vv                       DEL PEAK 45(20P12.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            271
[1] 2 2
[1] FALSE

Clustering(70) Variable = DEL PEAK 46(21Q11.2) MUTATION ANALYSIS
D70V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 46(21Q11.2) MUTATED   158  45
  DEL PEAK 46(21Q11.2) WILD-TYPE 308  83
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                           203                            391 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                            45                             83 
$`DEL PEAK 46(21Q11.2) MUTATED`
TCGA-A6-4105 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3552 TCGA-AA-3556 TCGA-AA-3560 
       14.53        19.07        34.03        13.02        23.01        19.99 
TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-A00L 
       19.00        36.00        14.93        31.07        24.03        38.04 
TCGA-AA-A00Z TCGA-CK-5912 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AG-3890 
       21.99        49.08        35.93        91.79        17.85        17.03 
TCGA-AG-4008 TCGA-AG-A01N TCGA-G5-6233 TCGA-G5-6641 TCGA-5M-AAT4 TCGA-5M-AATE 
       17.03        31.00        18.28        26.43         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5659 TCGA-A6-5664 
       43.76        43.76        42.28        37.05        30.44        22.09 
TCGA-A6-5665 TCGA-A6-5667 TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6653 TCGA-A6-6654 
       22.06        29.16        20.61        21.76        24.39        23.87 
TCGA-A6-6782 TCGA-A6-A567 TCGA-A6-A5ZU TCGA-AA-3488 TCGA-AA-3511 TCGA-AA-3517 
       20.28        61.84         9.63         5.03         6.97        38.99 
TCGA-AA-3519 TCGA-AA-3526 TCGA-AA-3538 TCGA-AA-3544 TCGA-AA-3660 TCGA-AA-3685 
        9.07        19.07        26.01        14.01        78.08        37.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3866 
       10.06        38.99        37.02        10.06         0.99        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3941 TCGA-AA-3955 TCGA-AA-3966 TCGA-AA-3968 
       27.02        18.05        24.00        20.98         2.01        21.99 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D 
        7.96        13.94        27.02        42.02        15.02        10.98 
TCGA-AA-A01F TCGA-AA-A01K TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02O 
       32.02        31.00        51.98        39.98         2.01         0.92 
TCGA-AA-A02W TCGA-AD-6890 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 
       41.00        24.53        22.42        26.47        16.44        14.50 
TCGA-AY-4070 TCGA-AY-4071 TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4616 TCGA-AZ-4684 
       16.31         0.95        17.85        19.33         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        12.69        12.46 
TCGA-CA-5797 TCGA-CA-6716 TCGA-CK-5914 TCGA-CK-6748 TCGA-CM-4744 TCGA-CM-4750 
       12.59        12.20        21.99         2.01        20.02         8.02 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 
       27.02        13.02        22.03        32.02         5.03        15.02 
TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 
       14.04        29.03        15.02        11.08        11.01        45.40 
TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6922 TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 
       17.75        25.48        10.13        12.43        14.30         9.04 
TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D6 TCGA-DM-A1D7 TCGA-DM-A1D9 TCGA-DM-A1DA 
       13.41        11.38        49.91        13.32       140.38         7.50 
TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 
      131.51        26.47        31.96        47.87         1.55        41.42 
TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6315 
       43.04        33.67         0.53        47.41         8.35        61.91 
TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV 
       36.00        26.43        46.75        18.18         9.93        42.77 
TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 
       60.13        46.92        39.48        17.23        37.97        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       24.36        20.02        24.59        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 
       12.00         7.07        36.03        24.00        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3881 
       34.03        12.03        19.99        20.98        29.98        19.04 
TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       19.99         1.02        48.03        19.99        36.03        14.04 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
        1.02         1.94        38.96        61.97        41.00        38.56 
TCGA-AH-6643 TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6157 
       43.20        13.78        48.20        21.01        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG 
       10.98        25.05        25.05       126.44        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6511 
       32.61         3.48         4.18        20.55        20.91        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       17.69        16.34        16.41        11.97         8.45        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 
        0.39        32.19        36.49        37.18        11.87 

$`DEL PEAK 46(21Q11.2) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 
       13.02        24.03        37.05        36.03         8.05         0.99 
TCGA-AA-3554 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3697 TCGA-AA-3713 
       17.95        19.99         6.05         0.92        85.05        19.04 
TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 TCGA-AA-3972 
       19.04        29.98        12.99        24.00         2.01        50.99 
TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 TCGA-AD-6888 
       26.01        24.00        19.07        39.06        21.37        15.52 
TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 TCGA-AZ-6601 TCGA-AZ-6608 
       25.08        10.88        75.95       106.75       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       26.17        79.69        10.39         8.02        13.94        19.99 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       25.97        15.95        36.03        51.98        21.24        55.76 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 
       15.62         4.80        12.66         9.53        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       42.90        44.91        35.11        16.57        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5662 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 
       29.19        33.53        23.61        32.71        27.09        22.52 
TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6780 
       24.13         8.38        25.08        25.18        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        56.25         7.04         3.02 
TCGA-AA-3494 TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 
        1.02        37.05        35.01        63.98         1.02         1.02 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 
        0.00        29.00        29.00        12.99        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         6.97 
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-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       15.02        11.01         5.98         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
        0.99        25.02         1.02        17.98        15.95        36.95 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3930 TCGA-AA-3947 
       32.05        31.07        53.00        31.00         2.01        33.01 
TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 TCGA-AA-3977 
       26.01        34.03        16.08        13.05        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00F 
       27.02        27.02        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-A00W 
       18.05        18.05         4.01         0.99        17.03        14.99 
TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01G TCGA-AA-A01I TCGA-AA-A01P TCGA-AA-A01Q 
       34.98        15.02        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         1.02        26.01        37.02 
TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AA-A03J 
        2.96         5.03        22.03        39.98        18.05        40.96 
TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 
       12.16        83.24         5.79        27.42         0.46         0.92 
TCGA-AU-6004 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L 
       27.09        33.01         0.20        21.44        17.82        17.26 
TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 TCGA-AZ-4614 TCGA-AZ-4615 
       18.84       109.28        58.39         1.41         5.65        32.94 
TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 
       22.36        62.79        88.21        49.41         6.77        11.74 
TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CA-6719 
       12.36        12.39        12.59        12.76        10.06        14.30 
TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 
       17.56       148.01        85.45        70.16        15.62        51.32 
TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 
       21.14        82.95       124.27        23.05        37.02        25.02 
TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5348 TCGA-CM-5349 TCGA-CM-5861 TCGA-CM-5863 
       26.04        29.06        22.98        30.08        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-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-6679 TCGA-CM-6680 TCGA-D5-5538 TCGA-D5-5539 TCGA-D5-5540 
       11.08        10.06        12.03        54.61        19.59        56.09 
TCGA-D5-5541 TCGA-D5-6529 TCGA-D5-6530 TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 
       55.92        20.19        20.42        18.25        43.27        15.12 
TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 TCGA-D5-6539 TCGA-D5-6540 TCGA-D5-6541 
       17.85         4.80        17.13        12.49        16.14        15.58 
TCGA-D5-6898 TCGA-D5-6920 TCGA-D5-6927 TCGA-D5-6928 TCGA-D5-6930 TCGA-D5-6931 
        7.53        12.39         9.44        11.64        13.35        12.00 
TCGA-D5-7000 TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 
       10.26       119.70        24.43        38.20       130.65        92.75 
TCGA-DM-A1D8 TCGA-DM-A1DB TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 
       12.59        44.32       135.65         7.76       139.17        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        35.74        35.74         6.18 
TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 
       34.42        13.25        35.31       133.18        82.39        74.56 
TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 
       67.30        65.85        53.62        44.68        55.04        85.48 
TCGA-G4-6311 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A50V 
       39.42        26.04        13.78        74.79        10.98        19.33 
TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX 
       19.33        15.65        12.79        16.80        29.46        32.98 
TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 
        8.42        31.30        21.90        38.70        11.90        70.03 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-A56L 
       43.04        13.55        34.49        37.74        16.83        65.98 
TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
       32.02        20.05         1.02        34.03         2.01        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        6.05         0.99        15.95         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
       32.98         0.99         0.99         1.02        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 
       13.02        35.01        14.01        25.02        32.02        28.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A032 
       23.01        37.02         9.07         1.02        49.97        38.04 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        2.50        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
       44.78        47.44        78.12         7.17        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       31.00        12.00        31.00        44.02        25.97        12.62 
TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 
       41.36       129.27        24.13        19.96        17.00        18.28 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
        9.96        49.51        28.57        19.66        38.14        12.46 
TCGA-G5-6572 
       47.08 

  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                          0.39                           0.00 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE 
                         21.76                          22.52 
[1] "0.4 - 140.4 (21.8)" "0.0 - 148.0 (22.5)"
[1] "hr=" "1.2"
D70V2, continuous
D70V3, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED   139  71
  DEL PEAK 46(21Q11.2) WILD-TYPE 309  91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED    139   71
  DEL PEAK 46(21Q11.2) WILD-TYPE  309   91
        clus
vv       DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  COLON                           139                            309
  RECTUM                           71                             91
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 46(21Q11.2) MUTATED        34        0       14        53         3
  DEL PEAK 46(21Q11.2) WILD-TYPE      70        1       23       119         9
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 46(21Q11.2) MUTATED           0         6          9         28
  DEL PEAK 46(21Q11.2) WILD-TYPE         2        18          6         56
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 46(21Q11.2) MUTATED           22       29         6         0
  DEL PEAK 46(21Q11.2) WILD-TYPE         33       34        18         2
D70V4, multiclass
            clus
vv           DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  STAGE I                              34                             70
  STAGE IA                              0                              1
  STAGE II                             14                             23
  STAGE IIA                            53                            119
  STAGE IIB                             3                              9
  STAGE IIC                             0                              2
  STAGE III                             6                             18
  STAGE IIIA                            9                              6
  STAGE IIIB                           28                             56
  STAGE IIIC                           22                             33
  STAGE IV                             29                             34
  STAGE IVA                             6                             18
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 46(21Q11.2) MUTATED     7  39 142  24
  DEL PEAK 46(21Q11.2) WILD-TYPE  13  66 275  45
D70V5, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  T1                            7                             13
  T2                           39                             66
  T3                          142                            275
  T4                           24                             45
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              N0  N1  N2
  DEL PEAK 46(21Q11.2) MUTATED   108  56  48
  DEL PEAK 46(21Q11.2) WILD-TYPE 238  94  67
D70V6, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  N0                          108                            238
  N1                           56                             94
  N2                           48                             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"
D70V7, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED   152  34
  DEL PEAK 46(21Q11.2) WILD-TYPE 301  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED    152   34
  DEL PEAK 46(21Q11.2) WILD-TYPE  301   54
   clus
vv  DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  0                          152                            301
  1                           34                             54
[1] 2 2
[1] FALSE
D70V8, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED    97 116
  DEL PEAK 46(21Q11.2) WILD-TYPE 192 209
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED     97  116
  DEL PEAK 46(21Q11.2) WILD-TYPE  192  209
        clus
vv       DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  FEMALE                           97                            192
  MALE                            116                            209
[1] 2 2
[1] FALSE
D70V9, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED   167  12
  DEL PEAK 46(21Q11.2) WILD-TYPE 315  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED    167   12
  DEL PEAK 46(21Q11.2) WILD-TYPE  315   17
     clus
vv    DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  NO                           167                            315
  YES                           12                             17
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 46(21Q11.2) MUTATED                    129
  DEL PEAK 46(21Q11.2) WILD-TYPE                  253
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(21Q11.2) MUTATED                               8
  DEL PEAK 46(21Q11.2) WILD-TYPE                            54
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 46(21Q11.2) MUTATED                      66
  DEL PEAK 46(21Q11.2) WILD-TYPE                    80
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 46(21Q11.2) MUTATED                                3
  DEL PEAK 46(21Q11.2) WILD-TYPE                             10
D70V10, multiclass
                                clus
vv                               DEL PEAK 46(21Q11.2) MUTATED
  COLON ADENOCARCINOMA                                    129
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 46(21Q11.2) WILD-TYPE
  COLON ADENOCARCINOMA                                      253
  COLON MUCINOUS ADENOCARCINOMA                              54
  RECTAL ADENOCARCINOMA                                      80
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 46(21Q11.2) MUTATED   152   3  14   7
  DEL PEAK 46(21Q11.2) WILD-TYPE 294   3  23  22
D70V11, multiclass
    clus
vv   DEL PEAK 46(21Q11.2) MUTATED DEL PEAK 46(21Q11.2) WILD-TYPE
  R0                          152                            294
  R1                            3                              3
  R2                           14                             23
  RX                            7                             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"
D70V12, continuous
D70V13, binary
                                cls
clus                               0   1
  DEL PEAK 46(21Q11.2) MUTATED     4 122
  DEL PEAK 46(21Q11.2) WILD-TYPE   1 230
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 46(21Q11.2) MUTATED      4  122
  DEL PEAK 46(21Q11.2) WILD-TYPE    1  230
                        clus
vv                       DEL PEAK 46(21Q11.2) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          122
                        clus
vv                       DEL PEAK 46(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            230
[1] 2 2
[1] FALSE

Clustering(71) Variable = DEL PEAK 47(21Q21.1) MUTATION ANALYSIS
D71V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 47(21Q21.1) MUTATED   156  41
  DEL PEAK 47(21Q21.1) WILD-TYPE 310  87
  DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE 
                           197                            397 
  DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE 
                            41                             87 
$`DEL PEAK 47(21Q21.1) MUTATED`
TCGA-A6-4105 TCGA-AA-3522 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3560 TCGA-AA-3688 
       14.53        37.05        19.07        34.03        19.99        19.00 
TCGA-AA-3692 TCGA-AA-3844 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-A00L TCGA-AA-A00Z 
       36.00        14.93        31.07        24.03        38.04        21.99 
TCGA-AZ-4681 TCGA-CK-5912 TCGA-G4-6314 TCGA-G4-6625 TCGA-NH-A8F7 TCGA-AG-3890 
      106.75        49.08        35.93        91.79        17.85        17.03 
TCGA-AG-4008 TCGA-AG-A01N TCGA-G5-6233 TCGA-G5-6641 TCGA-5M-AAT4 TCGA-5M-AATE 
       17.03        31.00        18.28        26.43         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2674 TCGA-A6-2678 TCGA-A6-2684 TCGA-A6-5659 TCGA-A6-5662 
       43.76        43.76        42.28        37.05        30.44        23.61 
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-3538 TCGA-AA-3544 TCGA-AA-3660 TCGA-AA-3685 
       38.99         9.07        26.01        14.01        78.08        37.05 
TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3842 TCGA-AA-3848 TCGA-AA-3856 TCGA-AA-3866 
       10.06        38.99        37.02        10.06         0.99        17.03 
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-A00O TCGA-AA-A00Q TCGA-AA-A01C TCGA-AA-A01D TCGA-AA-A01F 
       13.94        27.02        42.02        15.02        10.98        32.02 
TCGA-AA-A01K TCGA-AA-A029 TCGA-AA-A02F TCGA-AA-A02H TCGA-AA-A02W TCGA-AD-6890 
       31.00        51.98        39.98         2.01        41.00        24.53 
TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-6196 
       22.42        26.47        16.44        14.50        16.31         0.20 
TCGA-AY-A69D TCGA-AY-A71X TCGA-AZ-4616 TCGA-AZ-4684 TCGA-AZ-6600 TCGA-AZ-6603 
       17.85        19.33         5.13        65.00        12.10        29.56 
TCGA-AZ-6605 TCGA-AZ-6607 TCGA-CA-5254 TCGA-CA-5256 TCGA-CA-5797 TCGA-CA-6716 
        5.23         3.19        12.69        12.46        12.59        12.20 
TCGA-CK-5914 TCGA-CM-4744 TCGA-CM-4750 TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 
       21.99        20.02         8.02        27.02        13.02        22.03 
TCGA-CM-5860 TCGA-CM-5862 TCGA-CM-5864 TCGA-CM-6163 TCGA-CM-6164 TCGA-CM-6170 
       32.02         5.03        15.02        14.04        29.03        15.02 
TCGA-CM-6677 TCGA-CM-6678 TCGA-D5-5537 TCGA-D5-6531 TCGA-D5-6533 TCGA-D5-6922 
       11.08        11.01        45.40        17.75        25.48        10.13 
TCGA-D5-6923 TCGA-D5-6924 TCGA-D5-6926 TCGA-D5-6929 TCGA-DM-A1D6 TCGA-DM-A1D7 
       12.43        14.30         9.04        13.41        49.91        13.32 
TCGA-DM-A1D9 TCGA-DM-A1DA TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6459 TCGA-F4-6460 
      140.38         7.50       131.51        26.47         8.61        31.96 
TCGA-F4-6703 TCGA-F4-6704 TCGA-F4-6806 TCGA-F4-6807 TCGA-F4-6808 TCGA-F4-6854 
       47.87         1.55        41.42        43.04        33.67         0.53 
TCGA-F4-6855 TCGA-G4-6295 TCGA-G4-6315 TCGA-G4-6317 TCGA-G4-6320 TCGA-G4-6626 
       47.41         8.35        61.91        36.00        26.43        46.75 
TCGA-NH-A50T TCGA-NH-A6GA TCGA-QG-A5YV TCGA-SS-A7HO TCGA-AF-2687 TCGA-AF-2689 
       18.18         9.93        42.77        60.13        46.92        39.48 
TCGA-AF-2690 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       17.23        29.98        24.36        20.02        24.59        86.63 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 
       11.84        12.00         7.07        36.03        24.00        46.03 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3725 
       34.03        34.03        12.03         6.05        19.99        20.98 
TCGA-AG-3728 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       29.98        19.04        19.99         1.02        48.03        19.99 
TCGA-AG-4001 TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       36.03         1.02         1.94        38.96        61.97        41.00 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-4749 
       38.56        43.20        13.78        48.20        21.01        25.05 
TCGA-DC-6155 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE 
       13.97        25.05        25.05       126.44        57.24       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6511 
       51.48        32.61         4.18        20.55        20.91        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       17.69        16.34        16.41        11.97         8.45        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 
        0.39        32.19        36.49        37.18        11.87 

$`DEL PEAK 47(21Q21.1) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 
       24.33        45.60        13.94        24.16         1.02        58.03 
TCGA-AA-3516 TCGA-AA-3520 TCGA-AA-3524 TCGA-AA-3525 TCGA-AA-3543 TCGA-AA-3552 
       13.02        24.03        36.03         8.05         0.99        13.02 
TCGA-AA-3554 TCGA-AA-3556 TCGA-AA-3562 TCGA-AA-3662 TCGA-AA-3672 TCGA-AA-3697 
       17.95        23.01        19.99         6.05         0.92        85.05 
TCGA-AA-3713 TCGA-AA-3715 TCGA-AA-3870 TCGA-AA-3939 TCGA-AA-3950 TCGA-AA-3952 
       19.04        19.04        29.98        12.99        24.00         2.01 
TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A024 TCGA-AD-6548 
       50.99        26.01        24.00        19.07        39.06        21.37 
TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-6601 TCGA-AZ-6608 
       15.52        25.08        10.88        75.95       100.01         1.94 
TCGA-DM-A285 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6310 TCGA-G4-6321 TCGA-G4-6586 
        5.88        28.21        23.51        63.62        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 
       26.17        79.69        10.39         8.02        13.94        19.99 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       25.97        15.95        36.03        51.98        21.24        55.76 
TCGA-3L-AA1B TCGA-4N-A93T TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2675 
       15.62         4.80        12.66         9.53        46.65        43.43 
TCGA-A6-2676 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-2685 TCGA-A6-2686 
       42.90        44.91        35.11        16.57        37.25        37.02 
TCGA-A6-3807 TCGA-A6-3809 TCGA-A6-3810 TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5657 
       34.65        32.75        36.53        32.45        32.91        31.63 
TCGA-A6-5660 TCGA-A6-5661 TCGA-A6-5666 TCGA-A6-6137 TCGA-A6-6138 TCGA-A6-6140 
       29.19        33.53        32.71        27.09        22.52        24.13 
TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 TCGA-A6-6652 TCGA-A6-6780 TCGA-A6-6781 
        8.38        25.08        25.18        24.69        20.12        19.66 
TCGA-A6-A565 TCGA-A6-A566 TCGA-A6-A56B TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 
       16.24        24.92        56.25         7.04         3.02         1.02 
TCGA-AA-3495 TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 
       37.05        35.01        63.98         1.02         1.02        19.07 
TCGA-AA-3529 TCGA-AA-3532 TCGA-AA-3534 TCGA-AA-3542 TCGA-AA-3548 TCGA-AA-3549 
        0.00        29.00        29.00        12.99        33.99        21.01 
TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3561 TCGA-AA-3655 TCGA-AA-3663 
       24.00        29.95        20.98        13.94        61.02         6.97 
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-3680 TCGA-AA-3681 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 
       15.02        11.01         5.98         5.03        26.99        35.05 
TCGA-AA-3818 TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3841 
        0.99        25.02         1.02        17.98        15.95        36.95 
TCGA-AA-3845 TCGA-AA-3846 TCGA-AA-3850 TCGA-AA-3851 TCGA-AA-3852 TCGA-AA-3854 
        0.00        17.03         0.00        33.07         0.00        36.03 
TCGA-AA-3855 TCGA-AA-3858 TCGA-AA-3864 TCGA-AA-3869 TCGA-AA-3877 TCGA-AA-3930 
       32.05        31.07        53.00        27.02        31.00         2.01 
TCGA-AA-3947 TCGA-AA-3949 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3973 TCGA-AA-3975 
       33.01        26.01        34.03        16.08        13.05        34.06 
TCGA-AA-3977 TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E 
       25.02        27.02        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         1.02        26.01 
TCGA-AA-A01Z TCGA-AA-A02E TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y 
       37.02         2.96         5.03         0.92        22.03        39.98 
TCGA-AA-A03F TCGA-AA-A03J TCGA-AD-5900 TCGA-AD-6889 TCGA-AD-6899 TCGA-AD-6963 
       18.05        40.96        12.16        83.24         5.79        27.42 
TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 TCGA-AY-4071 TCGA-AY-5543 TCGA-AY-6197 
        0.46         0.92        27.09         0.95        33.01        21.44 
TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A8YK TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4323 
       17.82        17.26        18.84       109.28        58.39         1.41 
TCGA-AZ-4614 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-5403 TCGA-AZ-5407 TCGA-AZ-6598 
        5.65        32.94        22.36        62.79        88.21        49.41 
TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5255 TCGA-CA-5796 TCGA-CA-6715 TCGA-CA-6717 
        6.77        11.74        12.36        12.39        12.59        12.76 
TCGA-CA-6718 TCGA-CA-6719 TCGA-CK-4947 TCGA-CK-4948 TCGA-CK-4950 TCGA-CK-4951 
       10.06        14.30        17.56       148.01        85.45        70.16 
TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5916 TCGA-CK-6747 TCGA-CK-6748 TCGA-CK-6751 
       15.62        51.32        21.14        82.95         2.01       124.27 
TCGA-CM-4743 TCGA-CM-4746 TCGA-CM-4747 TCGA-CM-4748 TCGA-CM-5341 TCGA-CM-5348 
       23.05        37.02        25.02        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 
       54.61        19.59        56.09        55.92        20.19        20.42 
TCGA-D5-6532 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6537 TCGA-D5-6538 
       18.25        43.27        15.12        17.85         4.80        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-D5-6932 TCGA-D5-7000 TCGA-DM-A0X9 
       11.64        13.35        12.00        11.38        10.26       119.70 
TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D0 TCGA-DM-A1D4 TCGA-DM-A1D8 TCGA-DM-A1DB 
       24.43        38.20       130.65        92.75        12.59        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-A28F TCGA-DM-A28G TCGA-DM-A28H TCGA-DM-A28K TCGA-DM-A28M TCGA-F4-6461 
       35.97        60.79       117.07        98.24        95.18        11.11 
TCGA-F4-6463 TCGA-F4-6569 TCGA-F4-6570 TCGA-F4-6805 TCGA-F4-6809 TCGA-F4-6856 
       35.74        35.74         6.18        34.42        13.25        35.31 
TCGA-G4-6293 TCGA-G4-6297 TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 
      133.18        82.39        74.56        67.30        65.85        53.62 
TCGA-G4-6306 TCGA-G4-6307 TCGA-G4-6309 TCGA-G4-6311 TCGA-G4-6322 TCGA-G4-6323 
       44.68        55.04        85.48        39.42        26.04        13.78 
TCGA-G4-6627 TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A5IV TCGA-NH-A6GB TCGA-NH-A6GC 
       74.79        10.98        19.33        19.33        15.65        12.79 
TCGA-NH-A8F8 TCGA-QG-A5YW TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 TCGA-QL-A97D 
       16.80        29.46        32.98         8.42        31.30        21.90 
TCGA-RU-A8FL TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       38.70        11.90        70.03        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 
       34.49        37.74        16.83        65.98        36.03        32.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 
       20.05         1.02        34.03         2.01        50.04         0.99 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       15.95         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       14.01        25.02        32.02        28.04        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A032 TCGA-AH-6547 
       37.02         9.07         1.02        49.97        38.04         2.50 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       27.55        26.43        19.46         6.05        33.17        44.78 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       47.44        78.12         7.17        26.04        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       31.00        51.98        10.98        44.02        25.97        12.62 
TCGA-DY-A1DC TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 
       41.36        24.13         3.48        19.96        17.00        18.28 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
        9.96        49.51        28.57        19.66        38.14        12.46 
TCGA-G5-6572 
       47.08 

  DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE 
                           0.2                            0.0 
  DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE 
                        140.38                         148.01 
  DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE 
                         21.99                          22.03 
[1] "0.2 - 140.4 (22.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1"  
D71V2, continuous
D71V3, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q21.1) MUTATED   137  71
  DEL PEAK 47(21Q21.1) WILD-TYPE 311  91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q21.1) MUTATED    137   71
  DEL PEAK 47(21Q21.1) WILD-TYPE  311   91
        clus
vv       DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE
  COLON                           137                            311
  RECTUM                           71                             91
[1] 2 2
[1] FALSE
                                vv
clus                             STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 47(21Q21.1) MUTATED        29        0       12        56         2
  DEL PEAK 47(21Q21.1) WILD-TYPE      75        1       25       116        10
                                vv
clus                             STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 47(21Q21.1) MUTATED           0         6          9         29
  DEL PEAK 47(21Q21.1) WILD-TYPE         2        18          6         55
                                vv
clus                             STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 47(21Q21.1) MUTATED           24       26         7         0
  DEL PEAK 47(21Q21.1) WILD-TYPE         31       37        17         2
D71V4, multiclass
            clus
vv           DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE
  STAGE I                              29                             75
  STAGE IA                              0                              1
  STAGE II                             12                             25
  STAGE IIA                            56                            116
  STAGE IIB                             2                             10
  STAGE IIC                             0                              2
  STAGE III                             6                             18
  STAGE IIIA                            9                              6
  STAGE IIIB                           29                             55
  STAGE IIIC                           24                             31
  STAGE IV                             26                             37
  STAGE IVA                             7                             17
  STAGE IVB                             0                              2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 47(21Q21.1) MUTATED     6  35 145  22
  DEL PEAK 47(21Q21.1) WILD-TYPE  14  70 272  47
D71V5, multiclass
    clus
vv   DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE
  T1                            6                             14
  T2                           35                             70
  T3                          145                            272
  T4                           22                             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 47(21Q21.1) MUTATED   103  55  50
  DEL PEAK 47(21Q21.1) WILD-TYPE 243  95  65
D71V6, multiclass
    clus
vv   DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE
  N0                          103                            243
  N1                           55                             95
  N2                           50                             65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q21.1) MUTATED   151  32
  DEL PEAK 47(21Q21.1) WILD-TYPE 302  56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q21.1) MUTATED    151   32
  DEL PEAK 47(21Q21.1) WILD-TYPE  302   56
   clus
vv  DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE
  0                          151                            302
  1                           32                             56
[1] 2 2
[1] FALSE
D71V8, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q21.1) MUTATED    99 110
  DEL PEAK 47(21Q21.1) WILD-TYPE 190 215
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q21.1) MUTATED     99  110
  DEL PEAK 47(21Q21.1) WILD-TYPE  190  215
        clus
vv       DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE
  FEMALE                           99                            190
  MALE                            110                            215
[1] 2 2
[1] FALSE
D71V9, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q21.1) MUTATED   159  13
  DEL PEAK 47(21Q21.1) WILD-TYPE 323  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q21.1) MUTATED    159   13
  DEL PEAK 47(21Q21.1) WILD-TYPE  323   16
     clus
vv    DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE
  NO                           159                            323
  YES                           13                             16
[1] 2 2
[1] FALSE
                                vv
clus                             COLON ADENOCARCINOMA
  DEL PEAK 47(21Q21.1) MUTATED                    128
  DEL PEAK 47(21Q21.1) WILD-TYPE                  254
                                vv
clus                             COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 47(21Q21.1) MUTATED                               8
  DEL PEAK 47(21Q21.1) WILD-TYPE                            54
                                vv
clus                             RECTAL ADENOCARCINOMA
  DEL PEAK 47(21Q21.1) MUTATED                      66
  DEL PEAK 47(21Q21.1) WILD-TYPE                    80
                                vv
clus                             RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 47(21Q21.1) MUTATED                                3
  DEL PEAK 47(21Q21.1) WILD-TYPE                             10
D71V10, multiclass
                                clus
vv                               DEL PEAK 47(21Q21.1) MUTATED
  COLON ADENOCARCINOMA                                    128
  COLON MUCINOUS ADENOCARCINOMA                             8
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 47(21Q21.1) WILD-TYPE
  COLON ADENOCARCINOMA                                      254
  COLON MUCINOUS ADENOCARCINOMA                              54
  RECTAL ADENOCARCINOMA                                      80
  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"
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 47(21Q21.1) MUTATED   149   3  13   6
  DEL PEAK 47(21Q21.1) WILD-TYPE 297   3  24  23
D71V11, multiclass
    clus
vv   DEL PEAK 47(21Q21.1) MUTATED DEL PEAK 47(21Q21.1) WILD-TYPE
  R0                          149                            297
  R1                            3                              3
  R2                           13                             24
  RX                            6                             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
D71V13, binary
                                cls
clus                               0   1
  DEL PEAK 47(21Q21.1) MUTATED     4 121
  DEL PEAK 47(21Q21.1) WILD-TYPE   1 231
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 47(21Q21.1) MUTATED      4  121
  DEL PEAK 47(21Q21.1) WILD-TYPE    1  231
                        clus
vv                       DEL PEAK 47(21Q21.1) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          121
                        clus
vv                       DEL PEAK 47(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  1
  NOT HISPANIC OR LATINO                            231
[1] 2 2
[1] FALSE

Clustering(72) Variable = DEL PEAK 48(22Q13.32) MUTATION ANALYSIS
D72V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 48(22Q13.32) MUTATED   166  52
  DEL PEAK 48(22Q13.32) WILD-TYPE 300  76
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            218                             376 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                             52                              76 
$`DEL PEAK 48(22Q13.32) MUTATED`
TCGA-A6-2681 TCGA-A6-2682 TCGA-A6-4105 TCGA-AA-3520 TCGA-AA-3522 TCGA-AA-3552 
       45.60        13.94        14.53        24.03        37.05        13.02 
TCGA-AA-3560 TCGA-AA-3662 TCGA-AA-3697 TCGA-AA-3860 TCGA-AA-3867 TCGA-AA-3870 
       19.99         6.05        85.05        31.07        24.03        29.98 
TCGA-AA-3939 TCGA-AA-3952 TCGA-AA-3972 TCGA-AA-3976 TCGA-AA-A00Z TCGA-AZ-6608 
       12.99         2.01        50.99        26.01        21.99         1.94 
TCGA-CK-5912 TCGA-DM-A285 TCGA-G4-6310 TCGA-G4-6625 TCGA-AG-3611 TCGA-AG-A00H 
       49.08         5.88        63.62        91.79        13.94        25.97 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-4N-A93T TCGA-5M-AAT4 TCGA-5M-AATE 
       21.24        18.28        26.43         4.80         1.61        39.45 
TCGA-A6-2671 TCGA-A6-2678 TCGA-A6-2679 TCGA-A6-2680 TCGA-A6-2683 TCGA-A6-3807 
       43.76        42.28        44.91        35.11        16.57        34.65 
TCGA-A6-3810 TCGA-A6-5657 TCGA-A6-5659 TCGA-A6-5660 TCGA-A6-5662 TCGA-A6-6138 
       36.53        31.63        30.44        29.19        23.61        22.52 
TCGA-A6-6650 TCGA-A6-6651 TCGA-A6-6654 TCGA-A6-A567 TCGA-A6-A56B TCGA-A6-A5ZU 
       20.61        21.76        23.87        61.84        56.25         9.63 
TCGA-AA-3511 TCGA-AA-3517 TCGA-AA-3519 TCGA-AA-3532 TCGA-AA-3538 TCGA-AA-3542 
        6.97        38.99         9.07        29.00        26.01        12.99 
TCGA-AA-3548 TCGA-AA-3549 TCGA-AA-3561 TCGA-AA-3666 TCGA-AA-3673 TCGA-AA-3681 
       33.99        21.01        13.94         2.01        50.04         5.98 
TCGA-AA-3685 TCGA-AA-3811 TCGA-AA-3837 TCGA-AA-3841 TCGA-AA-3842 TCGA-AA-3846 
       37.05        10.06        38.99        36.95        37.02        17.03 
TCGA-AA-3848 TCGA-AA-3851 TCGA-AA-3855 TCGA-AA-3856 TCGA-AA-3858 TCGA-AA-3866 
       10.06        33.07        32.05         0.99        31.07        17.03 
TCGA-AA-3869 TCGA-AA-3875 TCGA-AA-3930 TCGA-AA-3966 TCGA-AA-3968 TCGA-AA-3973 
       27.02        18.05         2.01         2.01        21.99        13.05 
TCGA-AA-3989 TCGA-AA-A004 TCGA-AA-A00F TCGA-AA-A00O TCGA-AA-A00Q TCGA-AA-A00U 
        7.96        13.94        34.03        27.02        42.02        17.03 
TCGA-AA-A00W TCGA-AA-A01C TCGA-AA-A01T TCGA-AA-A01X TCGA-AA-A01Z TCGA-AA-A02F 
       14.99        15.02        33.04        26.01        37.02        39.98 
TCGA-AA-A02W TCGA-AA-A03J TCGA-AD-6899 TCGA-AD-6901 TCGA-AD-6965 TCGA-AD-A5EK 
       41.00        40.96         5.79        22.42        26.47        16.44 
TCGA-AU-3779 TCGA-AY-4070 TCGA-AY-5543 TCGA-AY-6196 TCGA-AY-A69D TCGA-AZ-4323 
       14.50        16.31        33.01         0.20        17.85         1.41 
TCGA-AZ-4614 TCGA-AZ-4616 TCGA-AZ-6600 TCGA-AZ-6603 TCGA-AZ-6605 TCGA-AZ-6607 
        5.65         5.13        12.10        29.56         5.23         3.19 
TCGA-CA-5254 TCGA-CA-5255 TCGA-CA-6716 TCGA-CA-6719 TCGA-CK-6748 TCGA-CM-4747 
       12.69        12.36        12.20        14.30         2.01        25.02 
TCGA-CM-4750 TCGA-CM-5341 TCGA-CM-5349 TCGA-CM-5862 TCGA-CM-5863 TCGA-CM-6170 
        8.02        29.06        30.08         5.03        15.02        15.02 
TCGA-CM-6677 TCGA-CM-6678 TCGA-CM-6679 TCGA-D5-5537 TCGA-D5-5540 TCGA-D5-6529 
       11.08        11.01        10.06        45.40        56.09        20.19 
TCGA-D5-6533 TCGA-D5-6534 TCGA-D5-6535 TCGA-D5-6536 TCGA-D5-6539 TCGA-D5-6898 
       25.48        43.27        15.12        17.85        12.49         7.53 
TCGA-D5-6923 TCGA-D5-6929 TCGA-D5-6932 TCGA-DM-A1D0 TCGA-DM-A1D7 TCGA-DM-A1D8 
       12.43        13.41        11.38       130.65        13.32        12.59 
TCGA-DM-A1D9 TCGA-DM-A1DB TCGA-DM-A1HA TCGA-DM-A28A TCGA-F4-6460 TCGA-F4-6704 
      140.38        44.32       131.51        26.47        31.96         1.55 
TCGA-F4-6807 TCGA-F4-6809 TCGA-G4-6295 TCGA-G4-6297 TCGA-G4-6309 TCGA-G4-6315 
       43.04        13.25         8.35        82.39        85.48        61.91 
TCGA-G4-6317 TCGA-G4-6626 TCGA-NH-A50T TCGA-NH-A50U TCGA-NH-A50V TCGA-NH-A6GA 
       36.00        46.75        18.18        10.98        19.33         9.93 
TCGA-QG-A5YV TCGA-QG-A5YW TCGA-QL-A97D TCGA-RU-A8FL TCGA-AF-2692 TCGA-AF-2693 
       42.77        29.46        21.90        38.70        13.55        37.97 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3575 TCGA-AG-3578 
       29.98        24.36        24.59        65.98        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3593 
        7.07        36.03        20.05        24.00        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 
       50.04        15.95        20.98        29.98        37.02        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        17.95         1.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       14.04         3.98        23.01         1.02         1.94        38.96 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6624 
       41.00        38.56        27.55         6.05        13.78        48.20 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
       21.01        25.05        31.00        13.97        10.98        44.02 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       25.05        25.05        41.36        51.48        32.61         4.18 
TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6810 
       20.55        17.69        16.31        16.41        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6863 
       36.49        11.87 

$`DEL PEAK 48(22Q13.32) WILD-TYPE`
TCGA-A6-2677 TCGA-A6-6649 TCGA-AA-3496 TCGA-AA-3506 TCGA-AA-3516 TCGA-AA-3524 
       24.33        24.16         1.02        58.03        13.02        36.03 
TCGA-AA-3525 TCGA-AA-3530 TCGA-AA-3531 TCGA-AA-3543 TCGA-AA-3554 TCGA-AA-3556 
        8.05        19.07        34.03         0.99        17.95        23.01 
TCGA-AA-3562 TCGA-AA-3672 TCGA-AA-3688 TCGA-AA-3692 TCGA-AA-3713 TCGA-AA-3715 
       19.99         0.92        19.00        36.00        19.04        19.04 
TCGA-AA-3844 TCGA-AA-3950 TCGA-AA-3979 TCGA-AA-3986 TCGA-AA-A00L TCGA-AA-A024 
       14.93        24.00        24.00        19.07        38.04        39.06 
TCGA-AD-6548 TCGA-AD-6888 TCGA-AD-6895 TCGA-AD-6964 TCGA-AZ-4313 TCGA-AZ-4681 
       21.37        15.52        25.08        10.88        75.95       106.75 
TCGA-AZ-6601 TCGA-G4-6294 TCGA-G4-6298 TCGA-G4-6314 TCGA-G4-6321 TCGA-G4-6586 
      100.01        28.21        23.51        35.93        22.09        35.80 
TCGA-G4-6588 TCGA-G4-6628 TCGA-NH-A8F7 TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 
       26.17        79.69        17.85        10.39         8.02        19.99 
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       17.03        17.03        15.95        36.03        31.00        51.98 
TCGA-G5-6235 TCGA-3L-AA1B TCGA-4T-AA8H TCGA-5M-AAT6 TCGA-A6-2672 TCGA-A6-2674 
       55.76        15.62        12.66         9.53        46.65        43.76 
TCGA-A6-2675 TCGA-A6-2676 TCGA-A6-2684 TCGA-A6-2685 TCGA-A6-2686 TCGA-A6-3809 
       43.43        42.90        37.05        37.25        37.02        32.75 
TCGA-A6-4107 TCGA-A6-5656 TCGA-A6-5661 TCGA-A6-5664 TCGA-A6-5665 TCGA-A6-5666 
       32.45        32.91        33.53        22.09        22.06        32.71 
TCGA-A6-5667 TCGA-A6-6137 TCGA-A6-6140 TCGA-A6-6141 TCGA-A6-6142 TCGA-A6-6648 
       29.16        27.09        24.13         8.38        25.08        25.18 
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-AA-3488 TCGA-AA-3489 TCGA-AA-3492 TCGA-AA-3494 TCGA-AA-3495 
       24.92         5.03         7.04         3.02         1.02        37.05 
TCGA-AA-3502 TCGA-AA-3510 TCGA-AA-3514 TCGA-AA-3518 TCGA-AA-3526 TCGA-AA-3529 
       35.01        63.98         1.02         1.02        19.07         0.00 
TCGA-AA-3534 TCGA-AA-3544 TCGA-AA-3553 TCGA-AA-3555 TCGA-AA-3558 TCGA-AA-3655 
       29.00        14.01        24.00        29.95        20.98        61.02 
TCGA-AA-3660 TCGA-AA-3663 TCGA-AA-3664 TCGA-AA-3667 TCGA-AA-3675 TCGA-AA-3678 
       78.08         6.97        54.02        14.01        47.05        47.01 
TCGA-AA-3679 TCGA-AA-3680 TCGA-AA-3696 TCGA-AA-3710 TCGA-AA-3812 TCGA-AA-3818 
       15.02        11.01         5.03        26.99        35.05         0.99 
TCGA-AA-3819 TCGA-AA-3821 TCGA-AA-3831 TCGA-AA-3833 TCGA-AA-3845 TCGA-AA-3850 
       25.02         1.02        17.98        15.95         0.00         0.00 
TCGA-AA-3852 TCGA-AA-3854 TCGA-AA-3864 TCGA-AA-3877 TCGA-AA-3941 TCGA-AA-3947 
        0.00        36.03        53.00        31.00        24.00        33.01 
TCGA-AA-3949 TCGA-AA-3955 TCGA-AA-3956 TCGA-AA-3971 TCGA-AA-3975 TCGA-AA-3977 
       26.01        20.98        34.03        16.08        34.06        25.02 
TCGA-AA-3982 TCGA-AA-3994 TCGA-AA-A00A TCGA-AA-A00D TCGA-AA-A00E TCGA-AA-A00J 
       27.02        27.02        38.04        19.00        30.02        18.05 
TCGA-AA-A00K TCGA-AA-A00N TCGA-AA-A00R TCGA-AA-A010 TCGA-AA-A017 TCGA-AA-A01D 
       18.05         4.01         0.99        34.98        15.02        10.98 
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-A029 TCGA-AA-A02E TCGA-AA-A02H 
       35.01         1.02         1.02        51.98         2.96         2.01 
TCGA-AA-A02J TCGA-AA-A02O TCGA-AA-A02R TCGA-AA-A02Y TCGA-AA-A03F TCGA-AD-5900 
        5.03         0.92        22.03        39.98        18.05        12.16 
TCGA-AD-6889 TCGA-AD-6890 TCGA-AD-6963 TCGA-AM-5820 TCGA-AM-5821 TCGA-AU-6004 
       83.24        24.53        27.42         0.46         0.92        27.09 
TCGA-AY-4071 TCGA-AY-6197 TCGA-AY-6386 TCGA-AY-A54L TCGA-AY-A71X TCGA-AY-A8YK 
        0.95        21.44        17.82        17.26        19.33        18.84 
TCGA-AZ-4308 TCGA-AZ-4315 TCGA-AZ-4615 TCGA-AZ-4682 TCGA-AZ-4684 TCGA-AZ-5403 
      109.28        58.39        32.94        22.36        65.00        62.79 
TCGA-AZ-5407 TCGA-AZ-6598 TCGA-AZ-6599 TCGA-AZ-6606 TCGA-CA-5256 TCGA-CA-5796 
       88.21        49.41         6.77        11.74        12.46        12.39 
TCGA-CA-5797 TCGA-CA-6715 TCGA-CA-6717 TCGA-CA-6718 TCGA-CK-4947 TCGA-CK-4948 
       12.59        12.59        12.76        10.06        17.56       148.01 
TCGA-CK-4950 TCGA-CK-4951 TCGA-CK-4952 TCGA-CK-5913 TCGA-CK-5914 TCGA-CK-5916 
       85.45        70.16        15.62        51.32        21.99        21.14 
TCGA-CK-6747 TCGA-CK-6751 TCGA-CM-4743 TCGA-CM-4744 TCGA-CM-4746 TCGA-CM-4748 
       82.95       124.27        23.05        20.02        37.02        26.04 
TCGA-CM-4751 TCGA-CM-4752 TCGA-CM-5344 TCGA-CM-5348 TCGA-CM-5860 TCGA-CM-5861 
       27.02        13.02        22.03        22.98        32.02        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-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-6680 TCGA-D5-5538 
       11.01        12.95        13.05        11.08        12.03        54.61 
TCGA-D5-5539 TCGA-D5-5541 TCGA-D5-6530 TCGA-D5-6531 TCGA-D5-6532 TCGA-D5-6537 
       19.59        55.92        20.42        17.75        18.25         4.80 
TCGA-D5-6538 TCGA-D5-6540 TCGA-D5-6541 TCGA-D5-6920 TCGA-D5-6922 TCGA-D5-6924 
       17.13        16.14        15.58        12.39        10.13        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        13.35        12.00        10.26 
TCGA-DM-A0X9 TCGA-DM-A0XD TCGA-DM-A0XF TCGA-DM-A1D4 TCGA-DM-A1D6 TCGA-DM-A1DA 
      119.70        24.43        38.20        92.75        49.91         7.50 
TCGA-DM-A1HB TCGA-DM-A280 TCGA-DM-A282 TCGA-DM-A288 TCGA-DM-A28C TCGA-DM-A28E 
      135.65         7.76       139.17        14.04        81.37       119.93 
TCGA-DM-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        35.74        35.74         6.18        47.87        34.42 
TCGA-F4-6806 TCGA-F4-6808 TCGA-F4-6854 TCGA-F4-6855 TCGA-F4-6856 TCGA-G4-6293 
       41.42        33.67         0.53        47.41        35.31       133.18 
TCGA-G4-6299 TCGA-G4-6302 TCGA-G4-6303 TCGA-G4-6304 TCGA-G4-6306 TCGA-G4-6307 
       74.56        67.30        65.85        53.62        44.68        55.04 
TCGA-G4-6311 TCGA-G4-6320 TCGA-G4-6322 TCGA-G4-6323 TCGA-G4-6627 TCGA-NH-A5IV 
       39.42        26.43        26.04        13.78        74.79        19.33 
TCGA-NH-A6GB TCGA-NH-A6GC TCGA-NH-A8F8 TCGA-QG-A5YX TCGA-QG-A5Z1 TCGA-QG-A5Z2 
       15.65        12.79        16.80        32.98         8.42        31.30 
TCGA-SS-A7HO TCGA-T9-A92H TCGA-WS-AB45 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       60.13        11.90        70.03        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K 
       43.04        34.49        37.74        16.83        20.02        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 
       11.84        36.03         1.02        46.03        34.03         2.01 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       12.03         6.05         0.99        19.99         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99         0.99        19.04        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4007 
       35.01        14.01        48.03        25.02        32.02         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 
       46.03        20.98        13.94         6.02        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
        1.02        49.97        61.97        38.04         2.50        43.20 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
       26.43        19.46        33.17        44.78        47.44        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
        7.17        26.04        12.00        31.00        51.98        25.97 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 
       12.62       126.44        57.24       129.27        24.13         3.48 
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-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-F5-6811 TCGA-F5-6813 
        8.45         9.96        49.51        42.35        32.19        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        12.46        47.08 

  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                            0.2                             0.0 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                         140.38                          148.01 
  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE 
                          21.99                           22.03 
[1] "0.2 - 140.4 (22.0)" "0.0 - 148.0 (22.0)"
[1] "hr=" "1.4"
D72V2, continuous
D72V3, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED   158  65
  DEL PEAK 48(22Q13.32) WILD-TYPE 290  97
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED    158   65
  DEL PEAK 48(22Q13.32) WILD-TYPE  290   97
        clus
vv       DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  COLON                            158                             290
  RECTUM                            65                              97
[1] 2 2
[1] FALSE
                                 vv
clus                              STAGE I STAGE IA STAGE II STAGE IIA STAGE IIB
  DEL PEAK 48(22Q13.32) MUTATED        29        0       10        57         1
  DEL PEAK 48(22Q13.32) WILD-TYPE      75        1       27       115        11
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 48(22Q13.32) MUTATED           0         8         10         31
  DEL PEAK 48(22Q13.32) WILD-TYPE         2        16          5         53
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA STAGE IVB
  DEL PEAK 48(22Q13.32) MUTATED           25       34        11         0
  DEL PEAK 48(22Q13.32) WILD-TYPE         30       29        13         2
D72V4, multiclass
            clus
vv           DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  STAGE I                               29                              75
  STAGE IA                               0                               1
  STAGE II                              10                              27
  STAGE IIA                             57                             115
  STAGE IIB                              1                              11
  STAGE IIC                              0                               2
  STAGE III                              8                              16
  STAGE IIIA                            10                               5
  STAGE IIIB                            31                              53
  STAGE IIIC                            25                              30
  STAGE IV                              34                              29
  STAGE IVA                             11                              13
  STAGE IVB                              0                               2
[1] 13  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 48(22Q13.32) MUTATED     4  37 157  27
  DEL PEAK 48(22Q13.32) WILD-TYPE  16  68 260  42
D72V5, multiclass
    clus
vv   DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  T1                             4                              16
  T2                            37                              68
  T3                           157                             260
  T4                            27                              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 48(22Q13.32) MUTATED   102  71  51
  DEL PEAK 48(22Q13.32) WILD-TYPE 244  79  64
D72V6, multiclass
    clus
vv   DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  N0                           102                             244
  N1                            71                              79
  N2                            51                              64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED   153  44
  DEL PEAK 48(22Q13.32) WILD-TYPE 300  44
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED    153   44
  DEL PEAK 48(22Q13.32) WILD-TYPE  300   44
   clus
vv  DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  0                           153                             300
  1                            44                              44
[1] 2 2
[1] FALSE
D72V8, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED   101 125
  DEL PEAK 48(22Q13.32) WILD-TYPE 188 200
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED    101  125
  DEL PEAK 48(22Q13.32) WILD-TYPE  188  200
        clus
vv       DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  FEMALE                           101                             188
  MALE                             125                             200
[1] 2 2
[1] FALSE
D72V9, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED   183   9
  DEL PEAK 48(22Q13.32) WILD-TYPE 299  20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED    183    9
  DEL PEAK 48(22Q13.32) WILD-TYPE  299   20
     clus
vv    DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  NO                            183                             299
  YES                             9                              20
[1] 2 2
[1] FALSE
                                 vv
clus                              COLON ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                    146
  DEL PEAK 48(22Q13.32) WILD-TYPE                  236
                                 vv
clus                              COLON MUCINOUS ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                              11
  DEL PEAK 48(22Q13.32) WILD-TYPE                            51
                                 vv
clus                              RECTAL ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                      61
  DEL PEAK 48(22Q13.32) WILD-TYPE                    85
                                 vv
clus                              RECTAL MUCINOUS ADENOCARCINOMA
  DEL PEAK 48(22Q13.32) MUTATED                                4
  DEL PEAK 48(22Q13.32) WILD-TYPE                              9
D72V10, multiclass
                                clus
vv                               DEL PEAK 48(22Q13.32) MUTATED
  COLON ADENOCARCINOMA                                     146
  COLON MUCINOUS ADENOCARCINOMA                             11
  RECTAL ADENOCARCINOMA                                     61
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               DEL PEAK 48(22Q13.32) WILD-TYPE
  COLON ADENOCARCINOMA                                       236
  COLON MUCINOUS ADENOCARCINOMA                               51
  RECTAL ADENOCARCINOMA                                       85
  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"
                                 vv
clus                               R0  R1  R2  RX
  DEL PEAK 48(22Q13.32) MUTATED   154   3  17  12
  DEL PEAK 48(22Q13.32) WILD-TYPE 292   3  20  17
D72V11, multiclass
    clus
vv   DEL PEAK 48(22Q13.32) MUTATED DEL PEAK 48(22Q13.32) WILD-TYPE
  R0                           154                             292
  R1                             3                               3
  R2                            17                              20
  RX                            12                              17
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V12, continuous
D72V13, binary
                                 cls
clus                                0   1
  DEL PEAK 48(22Q13.32) MUTATED     3 123
  DEL PEAK 48(22Q13.32) WILD-TYPE   2 229
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 48(22Q13.32) MUTATED      3  123
  DEL PEAK 48(22Q13.32) WILD-TYPE    2  229
                        clus
vv                       DEL PEAK 48(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           123
                        clus
vv                       DEL PEAK 48(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   2
  NOT HISPANIC OR LATINO                             229
[1] 2 2
[1] FALSE
